Though this may have changed, the only usable TG16 emu that I'd seen was shareware (and if memory serves they wanted quite a bit for it). I haven't really been following TG emulation much, as I didn't have much familiarity with the system.
The Genesis, however, has a much larger following in the emulation community. As such, the emulators for it are a good deal more mature and run most games. My favorite is the Windows-based DGen.
Also another system with a large following. The best emulators I've seen have been Boycott and (my favorite) NO$GB (which you have to register). As far as compatibility goes I haven't really seen anything that beats No$GB, hence why I feel more inclined to recommend it.
Emulators exist for it, though I've never used one. It's a newer system as well, so I'd imagine the emus aren't very advanced yet.
The GBA can be emulated quite well by Boycott Advance though you'd need a rather fast system to get any degree of performance out of it.
I suppose, if I were to pick one, I'd go with Genesis emulation, if only because of the maturity of the emulators.