-No dust in beta
-Different powerup sound in beta
-No release sound in beta
Well, something else which I wish to mention is another difference I noticed. This difference isn't listed in the "Comparisons" section of the website, also searching the boards returns no past posts about this. The difference is the amount of power output by a fully-charged spindash. This is probably already known, but I felt it was still worth mentioning just in case.
Something I always noticed but never said anything about was that a fully-charged spindash in the beta seemed to release slower and have less power than a fully-charged spindash in the final. So, I set up a little test to see if my observations were correct, or if I was just seeing things.
First, I opened two instances of Gens. Then I opened Green Hill Zone act 1 in both emulators; one from the beta, one from the final. In both versions, I positioned Sonic in the exact same position at the bottom of the first quarter-arc in the level (Right below the raised area with the palm trees). Then, one at a time, I did a full charge to do a spindash, then released, and compared how high Sonic shot up into the air.
First I did the beta. Upon release, Sonic shot up into the air about as high as the bottom coconuts in the shorter of the two visible palm trees.
Next, I did the final. Upon release, Sonic shot much higher, just short of passing the height of the taller palm tree.
If interested, you can see a video capture of this experiment here (1.4MB). Forgive the poor quality. Regardless of the fact that I did save it as DivX, my video editor SUCKS.
As I said earlier, this is most likely already known, but just in case I thought I should post about it, given I found no other references to this phenomenon anywhere on this site or these boards.