Best Quality Polish: Epic Games (at least for the Unreal Tournament series). I don't recall a notable bug, ever, and they patched the games more to add content\features than to firefight technical problems.
Innovative Ideas: Particle Systems. Independence War, despite being sci-fi, used actual physics in its gameplay which you could take advantage of with your ship's secondary thrusters. Not only that but the branching storyline was extensive and well-written for a space combat game. Your in-mission actions had consequences normally reserved for the RPG genre. While Wing Commander did do this first, the ongoing story was a fairly black and white affair in comparison.
Gameplay: Creative Assembly. Their more recent games have been flawed (mostly in the AI department), but I still remember being hooked on Shogun Total War for hours because of the excellent blend of turn-based\real-time elements, and challenging AI. Not to mention the underused setting.
Length: Too difficult to choose one here, quite a few games I've played were long without wearing out their welcome, or have had excellent replay value through multiplayer\mods.
Story: Obsidian Entertainment (I would say Black Isle, but most of them went to OE including what was left of Troika). I can't really fault their storytelling, and the choice & consequence elements are almost always top notch (apart from Dungeon Siege 3 that is).
Optimization: Again I think this goes to Epic for the excellent scalability of UE1 and 2/2.5. You could even run UT2004 on a 32MB Radeon, Geforce 2 GTS, the GF4\Radeon 9000 series IGPs, or even Intel\VIA\SiS IGPs with software rendering which was still playable.