I'm sorry, but that's way off. I counted them just this week, winnowing down the
Prestige Class Index on Wizards of the Coast's website to include only those published since the 3.5 revision.
There were 524.
I mean, yes, that's a big number, but it's nowhere near 1,000. Hell, even before you cut the list down Wizards of the Coast only lists 762 - and if you eliminate those pre-revision prestige classes that were reprinted in the
Complete series and elsewhere, I think the true number is more like 600.
Again, that seems like a lot - but D&D is the world's biggest and most popular roleplaying game, so it's no suprise to me that they publish a lot of material. If you balanced the number of D&D characters being played against the options available, and compared the results to a similar examination of the number of GURPS, Hero, World of Darkness, Palladium, or Unisystem characters being played balanced against the options available in those games, I bet that there wouldn't be a relative excess of options in D&D.