Based on what? There are so many factors you could weigh in on.
Quality? Okay, but my experience is that the best products are put out by companies that don't seem to keep up that value.
Ideas? Again.
Quantity? I wouldn't use that as a criteria itself, but it is too hard to judge a company with too few products.
Format? Atlas has the best format, I think. But they have no single product that has really knocked my socks off yet.
Anyways, in my very general estimation, I think it is safe to name (in no particular order):
Green Ronin: Thought their shipping schedule is a little light, their idea content and rules knowledge seems to be very high, and their books are invariably useful to me.
Sword & Sorcery Studios: Delivers a lot of material for the money, good ideas, good editing, and highly adaptable.
Fiery Dragon: The BEST modules IMO. A lot of character in a lot of their modules, and they seem to listen well to feedback, and have some very strong products on their lineup.
Right now I wouldn't put AEG here yet, but I think they are strongly poised to get there. Rokugan was a simply fantastic product. Undead, War and Monster show that they are still improving the format and style of their general D20 books (Monster is clever and quite a value to boot.) And they are well poised to move more fantastic d20 games onto the market in the near future like Spycraft and Farscape (holding my breath here...)