There are more non d20 systems games going strong out there than I can possibly mention but here's a few of my favourites (leaving aside any d20 and WW games):
Tribe 8 by Dream Pod 9 - Great dark post apocalyptic fantasy game that uses the Silhouette system. Dream Pod 9 do a whole range of games.
Mechanical Dream by Steam Logic - The most innovative and original fantasy game I have read.
Agone by Multisim - The French take on fantasy RPGs. Very evocative.
Warhammer Fantasy Roleplay by Hogshead Publishing - Its an oldie but still strong. Hogshead also do SLA Industries and Nobilis.
Blue Planet v2 by Fantasy Flight Games - Excellent sci fi game with a nice balance between playability and hard crunchy bits.
Unknown Armies by Atlas Games - Pulp Fiction meets Horror. Atlas games do a whole range of games.
Godlike by Hobgoblynn Press - WW2 superheroes with an innovative rule set.
Call of Cthulhu by Chaosium - Still going strong especially since WotC jumped on board with CoC d20.
Fading Suns by Holistic Design - Very popular and has a good d20 book if you don't want to use their system.
Also Seventh Sea, Legends of the 5 Rings, Deadland, All Flesh Must Be Eaten, Witchcraft, Little Fears, Whispering Vault, Kult, Hong Kong Action Theatre, Stormbringer and many many more...
Check out
RPGnet for a good RPG website that supports a wide range of games.