I think both the TG16 and Genesis sound hardware do their respective jobs just fine. Cases can be made for excellent works on both systems. Take Ghouls N' Ghosts, for example... clearly it sounds better on the Genesis than on the SuperGrafx. Now look at Street Fighter II... you've got to be deaf not to hear the PC-Engine version sounds better. Then there were the dual-platform games where it's a bit more subjective. Devil's Crush, for example, sounds better to me on the TG16, despite it being programmed, on the Genesis, by the mighty Technosoft. Kyokyuko Tiger/Twin Cobra sounds better, to me, on the Genesis. Cadash, while both versions sound different, seem altogether about the same quality. The list could go on and on... Of course, each system has their sound masterpieces. You'll never find anything like Streets Of Rage or Thunderforce on the TG16/PCE, and you'll never find anything like Soldier Blade or Aldynes on the Genesis. The TG16 didn't have FM channels for that low, thumping, twangy bass and the Genesis did not have custom waveforms or enough PSG channels to get the same kind of sound out of its PSG channels as the TG16. The only thing I wish they'd done with the PCE/TG16 is give the PSG channels their own controller chip to take a little heat off the CPU. I mean, it's not like full-blown PSG sound eats up a *lot* of CPU time (5-10% maybe), but every little bit counts.
As for NES games sounding better, there are two things in play here. The first is nostalgia and the second is musical composition. While an argument can be made that many NES games (Ninja Gaiden, Contra, SMB, Megaman) had some ultra-addictive stick-in-your-head tunes that you keep humming all day, I think the majority of what's going on is that it's nostalgia at work. You were younger, things made a bigger impression on you back then, and NES music was essentially a soundtrack to your youth.