I know there are many of you out there who have some sort of Fetish for this kind of thing, so I figured we could make a list of known isometric games that are good.
I'll contribute some easy ones to the list, like Fallout, Fallout 2.
But here's one that hasn't been released yet, but is getting some pretty good reviews
http://www.1up.com/do/reviewPage?cId=3170205]Sonic Chronicles: The Dark Brotherhood (Nintendo DS)
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The Disgaeas.
[url=http://en.wikipedia.org/wiki/Disgaea:_Hour_of_Darkness]http://en.wikipedia.org/wiki/Disgaea:_Hour_of_Darkness[/url]
First one is being re-released on DS, already out on PS2 and PSP. Some of the finest turn-based gaming ever.

Most of late 90' rpgs i.e Baldur's Gate, Icewind Dale, Planescape, Diablo etc

I admit, I am one of those with a fetish for these types of games. Here are some off the top of my head that are non RTS/ turn based strategy. Also not counting any "traditional" console rpg as they are all pretty much this perspective.
---PC---
Baldurs gates
Arcanum
soldiers
Fallouts
Diablos
Titans Quest
Syndicate
Freedom Forces
commandos
Never winter nights
Planescape
Icewind dales
---Console/handhelds---
Zeldas (except 2)
Legacy of kain
Secret of mana
Neutopias
Ys 1 and 2
Shadowrun
Robin Hood
Ikari Warriors
Commando
Soulblazer
Illusion of gaia
Final fantasy Adventure
I'll add more when I think of them...

Crusader: No Remorse
Crusader: No Regret

OMG thank you for reminding me of the names of those Crusader games! I loved them but could never remember the name!!
I'll also contribute X-COM here.

Technically speaking a lot of the games you mentioned aren't Isometric Stompy.
There was never an Iso Zelda game... I know Ikari Warriors wasn't either... and FF Adventure was the gameboy game right..? That wasn't Iso. Same as Secret of Mana. lol I know my post is pretty pointless.. but.. just sayin.

Aside from those listed: Spiderweb's Avernum series

Anyone else ever play Gender wars?

I thought that was a real life game... I war with females everyday... *sighs*

What you mean there's a video game!?

I lol'd!

i did ! i added to the Wish list thread ;)
awesome game !
as for this thread : don"t forget to mention Little Big Adventure and the sequel, Little Big Adventure 2 :D
adit : please add also Sanitarium !

Well, Ikari 2 was iso, although that was the least well-known of the series.
I see that nobody's mentioned Ultima 7 and 8. They deserve a place on the list.

Um...neither NWN or LoK are isometric, Stompy. Neither are any of the Zelda games I've played. NWN and most of the LoK are forms of 3rd person 3D. Blood Omen (IIRC) is a kind of top-down with sprites showing side-view that is often used in console games (Zelda 1, for instance). That is not isometric. Isometric refers to a game like BG, where everything in the world is turned and viewed from a diagonal fixed perspective.
There is actually an even more technical definition that is used for drafting in this perspective, so that, really, very few games are actually isometric. However, this is how the word is used in the gaming world.