Well, the main difference is how it's administered. Topical versions (gel, cream, patch) have to be applied daily, sometimes more than once a day. Gel dries quicker. Cream may have a less offensive odor to some, and be less drying to the skin. Some people say that topical T is not as effective in transmen who have not had hysto, but I don't know if that claim is substantiated or not.
Sub-Q and IM are both injections. Sub-Q has the advantage of using smaller needles, but I've been told it's "a PitA". Unfortunately, I never could get anyone to elaborate on exactly what they meant by that.
As far as IM injections go, I believe the difference is primarily geographical. Testosterone Cypionate is the most often prescribed version in the U.S., and Sustanon® is most often prescribed in Europe. The makers of Sustanon® also claim that it causes less water retention and estrogenic side effects. In Europe there is also a variety that only needs to be administered every few months, but to my knowledge it has not been approved in the U.S.
Another difference you may find is in the type of oil used to suspend the T. If you have any known allergies, or if you have an adverse reaction at the injection site, you may want to shop around for a different formulation. Also, compound pharmacies, like Strohecker's, can change out the type of oil they use. Some people have also reported an increase or decrease in acne depending upon the type of oil used.
I've heard of body builders using Testosterone Enanthate, but I have never come across a trans guy who was using it, so I can't tell you much about it. I know that chemically it is very similar to Testosterone Cypionate, and I've heard body builders say that one seems to react better in some people's bodies than the other, but I don't know why, or why doctors almost always prescribe Test C (in the U.S.)
In addition there are a few oral versions, but early oral versions were very toxic to the liver, and in any case the T gets broken down more going through the digestive system, so they are rarely prescribed.
There is also a pellet system, similar to Birth Control implants, that require minor surgery, but only have to be dealt with every few months.
I hope that was helpful.
