If I look back to my 'original Amiga-days' I have spent most time at games published by Core Design. They have published high quality games in almost every genre that was available: RPG, Racing, Platform, Adventure and so on. Add to this some classics like Rick Dangerous, Chuck Rock and Heimdall and Core definitely get my vote.
Thalion, Cinemaware and Psygnosis are good runner ups.
I have never understood why everyone ever hails Team 17. Sure, their games had lots of depth and pushed the Amiga to its limits, but I found their games always 'clinical' -I cannot find another word for it.
My contender for 'Worst softwarehouse -ever' is Free Spirit Software. They produced rubbish like Sex Vixens from Outerspace and Bravo Romeo Delta -but maybe this is for a possible Worst-softwarehouse -thread.