Oo this is good question...
For myself i would have to categorise it as follows:
Best non D20, for Theme and System:
1)FASA's Earthdawn (excellent game, though it had perhaps the worst cover and PR of any RPG i've known).
2) Cyberpunk 20.20 by R.Talisorean (had a few flaws, but just rocked from start to finish)
3) Wasteworld, can't recall who published this, some Yugoslavian company i think. but it was excellent, though either went unnoticed, ro unappreciated as there hasn't been aything new for it a long time.
Best non D20, for Theme, though system was not upto scratch
1) Mechwarrior by FASA (created to complement the Battletech tabletop game, this had depth and history and color in the bucket load, but the RPG system was a little disappointing).
2) Pendragon by chaosium (Arthurian game, usual % system of the original Cthulhu, not the best system, but the topic was so colourful and detailed, this book was more like a history book for RPg'er..great stuff).
3) RIFTs & Robotech etc.. by Palladium (These guys have some of the best ideas and artwork in any games, but have no sense of game balance, and THE worst system ever, pity really, they have half of perfection and then refuse to listen to reason)
4) Traveller, original (Great game,oodles of history and depth and feel, but the system in some additions needed a maths degree to cope with...still it's endeared to enough people to have always made a comeback, and you can't fault that in a game)
5) Stormbringer by Chaosium (the Original Hardback version, again used the % cthullhu system, but this game gave the feel of the books, had some wonderful pullouts and was well made and written)
6) Warhammer Fantasy Roleplay by Games Workshop (again had a lovely world most of us grew up with, excelent artwork as only GW do, but the system was a lazy conversion of thier tabletop game and was a basic % system... still if they had ever released a WH40K version i'd still have bought it <g>)
7) Shadowrun by FASA (excellent background and feel, and setting, but definitely a bucket of dice system, still it is playable despite that fact)
8) Vampire, Werewolf etc.. by White Wolf (excellent themes, and productions, good art mixed with terrible art, but once again bucket of dice systems, although again still remained playable)
9) Gamma World 4th by TSR (the Last edition of Gamma World sadly were ever going to see seemingly, the PA setting is the untapped market along with the superhero genre, as far as good systems and settings go, but this was as good as it gets..so why is it here and not in the first list....well because it's out of print, damned hard to find, and unlikely to reappear despite its loyal fanbase).
10) Marvel Super Heroes by TSR (again awful system, but totally loyal to the theme and feel of the comics, good artwork and bucket loads of feel, but perhaps one of the worst systems ever to be thought up.. still i wish they'd remake a D20 version, pretty please, or someone buy Marvels license and do it<g>)
and thats off the top of my head, and a glance at my gaming collection in sight <g>
