Apples have the widest choice of rootstock selections.

Once you know your system, site and soil, then rootstock choice follows.

Listed in approximate order of dwarfing / size control--- results can vary with your site and the vigor of grafted scion.  This is not an all inclusive list.  New ones are still being introduced, and there are many others which have not made it successfully into commercial useage.

Bud 9  (Budagovsky 9) [30-35%]--- This is a very hardy apple rootstock that is gaining in popularity.  Produces a full dwarf tree (approx 30-35% of standard).  Grower experience is teaching us that it may be one of the weaker commercially suitable dwarfing roots, so growers need to make sure that they work to have young trees grow and reach the top trellis wire before fruiting too hard.  Being "greedy" and fruiting too early and hard may create "runting" problems that will have to be addressed.  Precocious.  Requires support--- staking or trellising.  Reported to be resistant to collar rot, powdery mildew and apple scab.  Very resistant to winter frost or damage.  Originally reported to be susceptible to fire blight, but experiences in 2000 in Michigan have indicated that it seems to be quite tolerant and much less susceptible than most other Malling 9. clones.   Does well in most soils, but irrigation is recommended in light soils.  Very good availability of most varieties on Bud 9.

M-9-337 (NAKB 9)[30-35%]--- This is one of the most commonly propagated and available Malling 9 clones from Europe and the standard to which most Malling 9 type rootstocks are compared to.  True dwarfing rootstock, 30-35% of standard.  Early cropping and precocious.  Requires support--- staking or trellising.  Tends to produce large fruit.  Tolerant of heavy soils.  Should only be used in light soils if adequate moisture or irrigation is provided, as it can tend to put all its energy into producing the crop and little into saving itself under drought conditions.  Found to be susceptible to fire blight damage.  Under a severe infestation, blight can travel to the root in the fall, resulting in tree decline and ultimate death next year or thereafter.  This is a great rootstock for high density planting in general, especially the highest densities.  Good availability of most varieties on M9-337.

M-9 Nic 29™  (USPP 10714- RN29) [35-40%]--- A selection of Malling 9 from Belgium suggested for cultivars with less vigor such as Empire or Honeycrisp.  Slightly more vigor than M-9-337 due to its more expansive and less brittle root system.  Still requires support, but tree survival is increased due to its more vibrant root system.  Becoming much more widely available.

M-9 Pajam #2 (USPP 7715-Cepiland) [35-40%]  A French selection of Malling 9 reported to be slightly more vigorous and productive.  May have better compatibility with more grafted varieties.  Some growing trials indicate better fruit coloring and size and earlier maturity also.  As hardy as other strains of M9.  Somewhat limited in availability at this time.
Geneva™ 11 [35-45%] --- One of the latest introductions from the Cornell University program for fire blight resistant rootstocks.  G 11 is now becoming more available and is recommended at this time for testing in comparison to the more vigorous "9" clones.  It is reported to be productive, with higher yield efficiencies than most commercial roots, including M9 clones.  It suckers only slightly and is only moderately susceptible to wooly apple aphid.  Fire blight resistance is excellent.  Limited to the most popular varieties at this time.
Geneva 16™ [35-45%] --- A newer introduction from Cornell University that shows promise.  Reported to be highly fire blight resistant.  Produces a tree size between M 9 and M 26.  Tolerant to collar rot and immune to scab.  Susceptible to powdery mildew and woolly apple aphid.  Reported to be well anchored and sucker free, but support is still recommended because it is precocious and productive.  G16 should only be budded or grafted to certified, virus-free scion wood due to its virus hypersensitivity!  Buds or grafts of virus infected wood will not "take" or the trees will decline rapidly.  We do not recommend it for home or farm self-propagation unless the grower is certain of the virus-free nature of his budwood.  Very limited availability at this time, and likely to be replaced by better Geneva(R) selections because of its virus-sensitiviity issues.  I look for it to essentially disappear from the marketplace in the future.  Limited to the most popular varieties at this time and recommended for testing at this time.  Being dropped by many nurseries because of virus sensitivity and potentially better roots.
EMLA 9 [35-40%]--- A slightly more vigorous clone of Malling 9 (35-40% of standard).  Otherwise, similar to other Malling 9 clones in most characteristics.  Not often used anymore as it has been replaced for the most part by other M9 strains or Bud 9.  Little to no availability as it is a less preferred than other 9 clones..
Geneva 41® [35-40%]--- One of the newest introductions.  Reportedly very fire-blight resistant and producing a tree similar to EMLA 9 but with better productivity.  Very winter hardy and has shown superior performance in most trials.  Very limited production of this rootstock make at this time make it hard to come by.
Geneva 202® [40-45%?]--- One of the newest introductions.  Reportedly very fire-blight resistant and highly resistant to wooly apple aphid.  Reported to produce a tree similar in size to EMLA 26.  Winter hardy and has shown superior performance in most trials.  Very limited production of this rootstock make at this time make it hard to come by.
Geneva 935® [40-45%?]--- One of the newest introductions.  Reportedly very fire-blight resistant and producing a tree as productive as M9.  Very winter hardy and has shown superior performance in most trials.  In the size range of EMLA 26--- so almost in the semi-dwarf range class, but support is highly recommended because of its precocity and potential heavy cropping issues.  Very limited production of this rootstock make at this time make it hard to come by.
VF EMLA 26  [40-50%]--- This is an excellent rootstock that produces a dwarf tree (approx. 40-50% of standard).  Tends to produce lots of large fruit, early on, and requires less support than Malling 9.  If trained to produce framework in the first few years before cropping, it can often support itself.  However, one would need to sacrifice a year or two of early production for framework growth.  Has good anchorage, but bud unions may tend to be slightly brittle.  Most bud unions exhibit a highly visible overgrowth of the rootstock, which is a normal characteristic of this rootstock.  Care needs to be taken to watch for possible scion rooting as this swelling often will start to touch the ground over time.   Likes lighter soils, but should be irrigated.  Refrain from planting in heavier soils, unless they are very well drained.  Not resistant to collar rot.  Highly susceptible to fire blight from sucker infestation as well as from downward movement of blight through the trunk from the scion.  It is susceptible to dogwood and other borers, so needs to be protected from infestation from borers.  One reported control method is to plant this rootstock at normal depth with the bud union well above the ground level, but then to mound dirt up around the bud union for 2-3 years until the bark becomes thick enough to resist borer penetration.  Then, remove the mounded dirt and cut any scion roots that may have developed to maintain size control.  Few suckers.   Ready availability on almost all varieties.
M-9/ EMLA 111 Interstem [40-50%]--- A common interstem combinations used by growers wishing semi-dwarf trees, but limited by their site.  The EMLA 111 is very adaptable to wetter, poorly drained sites, while the M-9 helps provide dwarfing and productivity.  Very limited in availability--- additional costs involved.
Geneva 30™ [45-55%] --- This new Geneva rootstock is notable for its excellent resistant to fire blight and crown rot.  Very precocious with fair anchorage.  Should have support because of its early cropping characteristics.  Approximately 50% of a standard tree.  This rootstock could be an excellent replacement for M 7 as it is in the same size category and is much more precocious.  Not widely available in the commercial fruit tree nursery trade because of several nursery production problems, but would be one to work with in a grower's own nursery if the need is for fire blight resistance in a semi-dwarf orchard.  Due to its "willowy" growth habit, rootstock producers have trouble grading high percentages of saleable, first grade rootstocks.  When lined out in the nursery, higher than normal liner losses can be expected--- reports up to 30%.  Makes a nice tree in the nursery after it has been budded, though.  Due to its nursery production characteristics G. 30 is expected to be replaced in the future with a more "nursery friendly" rootstock from Geneva.  Not readily available, limited to highly blight susceptible varieties typically.
VF EMLA 7 [50-60%] --- This virus-free clone of Malling 7 has proven itself to be one of the most popular rootstocks in the commercial industry, mostly due to its approx. 50-60% of standard size.  It tolerates a wide range of soils that are well drained, but does best with adequate moisture thru the summer.  Moderately resistant to collar rot.  Somewhat susceptible to fire blight, especially on younger trees if the blight enters the root.  When tree is older and less vigorous, blight is much less of a worry.  Excellent winter hardiness.  Only moderately well anchored.  Older trees tend to start leaning and tipping unless supported.  Fruit size is adequate, but not as large as M 9 or 26.  This is an excellent beginners rootstock because of its versatility.  It was once a very popular rootstock in Michigan, but many growers are looking for a replacement in the same size range because of its annoying suckering and leaning habits.  Very popular and almost all varieties are available on EMLA 7.
EMLA 106 [60-70%]--- This virus-free clone of Malling 106 is again gaining favor in Michigan in areas with lighter, sandier, well drained soils.  Approx. 60-70% of standard.  Well anchored and deep rooted.  Does not sucker.  Supports itself well.  Susceptible to collar rot, especially in poorly drained areas or soils.  Susceptible to fire blight.  Resistant to wooly apple aphid.  Gaining favor over Malling 7 in Michigan by growers wanting semi-dwarf, free-standing orchards in spite of its slightly larger size or who do not want to make the higher investment into higher density plantings.  Somewhat limited in availability of varieties budded to EMLA 106.
EMLA 111 [75-85%] --- This virus-free clone of Malling 111 produces a tree approx. 75-85% of standard depending on soil conditions.  Many consider it a "standard" size tree.  Well anchored and self supporting.  Under wetter soil conditions, which it tolerates very well, it is somewhat shallow rooted, and will make a larger tree.  Under sandier soil conditions, it is less vigorous, but grows well.  This is a good rootstock for growers wanting larger semi-dwarf orchards or for sites with replant problems which are limiting tree vigor.  Not highly used by a lot of commercial orchardists because of its almost standard size tree.  Good availability of many varieties on EMLA 111, especially low vigor varieties.
Bud 118 (Budagovsky 118) [80-85%?]--- Similar in size to EMLA 106 and 111.  Very winter hardy and adaptable to a wide range of soils.  Resistant to collar rot.  Unknown susceptibility to fire blight.  Reported to be as precocious as EMLA 106.  Some growers are experimenting with planting this at higher densities, hoping that its precocity and productiveness will help "dwarf" the tree into a more semi-dwarf class.  There are some reports that it may have a "tipping, leaning or anchorage" problem, even though it appears to have an excellent root system.  Becoming widely available.
Domestic Seedling [Standard 100%]--- Hardy used anymore in the commercial orchard except for the extreme low vigor varieties like spur red delicious.  The only  rootstock which was available to Great Grand Dad.  He didn't seem to mind waiting four to eight years to pick his first fruit and then climbing 20 to 40 foot tall trees and picking apples!  Widely adaptable to all soil types.  Produces great fire wood in about 50 years!  Virtually no availability. 

Observations and Opinions about the Geneva® Rootstock Series:
On a trip visiting the nurseries I work with in Washington in Fall of 2012, I tried to focus on the new Geneva roots.  For the past several years, many researchers have been touting them as if they are "the next best thing to sliced bread!"  This may turn out to be the true in the long-run, but in the meantime, they have generated so much over-excitement and over-expectation in both new and established growers, that demand for them has so far out-paced production that it is almost impossible to ever find any varieties speculatively budded onto them for sale to growers.  Almost all the Geneva roots produced are being contracted to orders placed 2-3 or more years in advance, and very little is ever budded without a pre-order or contract in place.  If speculated on, they are budded onto a "sure sale" like Gala or Honeycrisp, and usually get sold as soon as they appear on an availability list.  So, new growers who may be getting advice to plant only Geneva, should take the real facts of life into account, and NOT expect to find readily available trees on any of the roots at this point in time.   

The rootstock nurseries are still in a steep learning curve in how to produce the Geneva rootstocks--- some of them have production problems that have to be overcome or learned to live with.  While tissue culture is a viable alternative, prices for tissue culture plants are much higher and nurseries must learn how to deal with the typically small tissue cultured plants in the nursery field.  In the fruit tree nursery, the nursery growers have their own learning curve in producing trees on the Geneva roots--- from dealing with small tissue cultured plants to keeping finished trees from breaking at the bud union on some Geneva clones.  In general, I would say that most of the Geneva clones I have experience with appear to have a more brittle nature than the older EMLA rootstocks, a characteristic that both nursery growers and fruit growers will have to learn how to deal with in some fashion.

      Don't get me wrong!  I believe that many of the Geneva rootstocks will prove to be excellent rootstocks for the future.  However, as with any "new" technology there are many things that need to be learned about it.  Cynics, such as myself, believe that we often are told about the good things first, then with time and experience we learn about the bad things.  Over time, we make the final judgments whether something "new and better" truly is such and how we have to change our methods to live with some of the lesser qualities that we may find disheartening.  The Geneva's, as well as other newly bred rootstocks from other parts of the world which are just starting to be introduced, will eventually make themselves successes or failures on their own merits, which will be discovered over years of testing and grower experience.  Some will fail, others will succeed. 
    Matt Moser