There have recently been some good threads about C64 and prior to the PCEngine games that everyone enjoys, you can check those out for some good recommendations for those systems. I understand where you're coming from, I don't want to miss out on a great game just because I didn't know about it either!
Some of my favorites:
C64 - Airborne Ranger, Trailblazer 2, lots more
PCE - Shinobi, Bomberman Series, Klax, PC Genjin (Bonk), Mesopotamia, Ninja Spirit and all the shooters.
SMS/GG - All the Sonics, Speedball II, MS Pacman, Streets of Rage, Marble Madness, Zoop, RPGs, Rygar, Rastan (cruddy conversion, but I LOVED the arcade game, will disappear if MAME can support it!), more...
NES - Donkey Kong, Ghosts 'n Goblins, Joust, Puzznic (its like Vexed for the GP32 if you liked that), Ninja Gaiden series, Super Spike Beach Volleyball, Spy Hunter, more...
SNES - Smash TV, Zombies Ate My Neighbors, Flashback, Magic Sword, F-Zero, Bubsy, Prince of Persia 2. Looking forward to many more as the emu improves, most of these run well enough one emu or the other.
GB/GBC - Haven't tried too many games, but there is a pong version I like here
Spectrum - Again, haven't tried many and don't know the system well, I enjoy 180 and Chuckie Egg from what I've tried. Dizzy games (here and C64) seem good also, haven't tried too much though.
MSX/MSX2 - Thexder and Firehawk (Thexder 2) - I'm biased based upon the hours on end I spent with Thexder growing up, but I LOVE the games; Gradius/Nemesis 1-3, Metal Gear 1 & 2, King's Valley 2 for MSX2, Aleste/Aleste Gaiden, Burgertime, Flicky, Loderunner 1&2 (graphics are bad, but work
), Arkanoid 1 &2, Penguin Adventure, Arctic Adventure, Vampire Killer (Castlevania).
GP32 games - My favorites are X-Rick, GP-Asteroids and Sokoban. Arcano was great but too short
. I haven't tried any commercial games yet, will be getting a few from JoyGP 1) in hopes they're decent and 2) to support the service, I think this is the one way GP32 has a chance with non-homebrew games, by exploiting the ability to download commercial games directly for less.