Nice lists! Mine are:
Mega Drive
1. Alien Soldier
2. Battle Mania Daiginjou
3. Phantasy Star IV
4. Bare Knuckle III
5. Shinobi III
Joint best 16 bit system alongside the PC Engine (fuck the SNES, overrated JRPG and slowdown machine). I think Bare Knuckle III is the best in the series. Shame they messed with it when they brought it over to the west. Sonic 1,2,3 & Knuckles, Streets of Rage 2, MUSHA, Gunstar Heroes, Alisia Dragoon, Shining Force II, Panorama Cotton, Revenge of Shinobi, Ristar, Thunder Force III and IV, Rocket Knight Adventures, Castlevania Bloodlines, Contra Hard Corps and Dynamite Headdy all almost made the list.
Mega CD
1. Sonic CD
2. Snatcher
3. Popful Mail
4. Lunar: The Silver Star
5. Final Fight CD
Very underrated system. Sonic CD is the best Sonic game and probably my favourite 2D platformer full stop. Snatcher is an amazing experience and tied first for my favourite Kojima game alongside the first MGS. Shining Force CD, Robo Aleste, Sol-Feace, Time Gal, Road Avenger and Keio Flying Squadron all nearly made the top five.
32X
1. Virtua Racing
2. After Burner II
3. Space Harrier
4. Knuckles Chaotix
5. Virtua Fighter
Pretty slim pickings here, these are pretty much the only good games on the system! Virtua Racing is a great port, better than the Saturn version, as is Virtua Fighter. In fact the 32X port of Virtua Racing is probably still the best one. Even better than the PS2 one, which has slightly dodgy handling. The 32X versions of After Burner II and Space Harrier are great and the best versions available at the time, but the Saturn versions came out a few years later and were completely arcade perfect, rendering the 32X versions a bit obsolete. Chaotix is a great game once you get the hang of it.
Saturn
1. Panzer Dragoon Saga
2. Virtua Fighter 2
3. NiGHTS Into Dreams
4. SEGA Rally
5. Virtual On
Very difficult for me to choose just 5, the Saturn is my favourite system of all time. Radiant Silvergun, X-Men vs. Street Fighter, Panzer Daragoon 1 and 2, Fighters Megamix, Bulk Slash, Daytona, Batsugun, Guardian Heroes, Shining Force III, Sengoku Blade, Deep Fear and Virtua Cop 2 all very nearly made the top 5. Wonderful system.
Dreamcast
1. Shenmue II
2. Jet Set Radio
3. Crazy Taxi 1/2
4. Capcom Vs. SNK 2
5. Shenmue
Probably my second favourite system of all time behind the Saturn. An arcade fanatic's dream, SEGA and Capcom arguably at their best. It seemed like every week a new batch of colourful brilliant games would come out. Bursting with creativity and new ideas. Rez, Soul Calibur, Power Stone 1 and 2, Chu Chu Rocket, Samba de Amigo, Marvel Vs. Capcom 2, Rival Schools 2, Ikaruga, Space Channel 5 1 and 2, Cannon Spike and Gunbird 2 almost made the list.