Here goes my list, in no particuar order:
Compile - Mainly for its MSX games, but also some of their 16 bits stuff were great. Made: Aleste series, Zanac series, Puyo-Puyo and a few other games
Konami - Again, mainly for their MSX stuff, but I think every system they touched, they made dozens of brilliant games. They aren't exactly the most "user-friendly" company ever, and they have made lots of things that makes them easily to be hated, but we have to agree, they've made LOTS of brilliant games.
Treasure - Cult japanese developer. Their finest hour was with the Mega-Drive, their line-up for the system is impressive: Gunstar Heroes, McDonald's Treasure Land (The only not so good title), Alien Soldier, Dynamitte Headdy, Lightining Cusader, Yuyu-Hakusho. Also made Radiant Silvergun and Guardian Heroes on Saturn, and Ikaruga on Dreamcast and Gamecube. Has made lots of other great games in many systems.
Sensible Software - Needs no introduction here
EVERYTHING they made on Amiga is golden. They surely are missed nowadays.
Team 17 -Again, no need for introduction. What's funny about Team 17 for me is that they don't have many "favourites" in my list (Most of their games have a better example in the same genre), but it's the only company that has released more than 20 games and ALWAYS kept the high quality on their releases.