If a mod decides to go the full 9 yards to fully get Steamworks in, Valve has been fairly OK with dumping them onto Steam.
Problem is Steamworks can be a hassle and a half to get in, and most good mods are going the indie route anyways to make money (or using Impulse from Stardock). Plus, most (i.e. all) of the mods they've let through are Steamworks standalone games that are free and use the Source Engine.
That being said, I have several mods that I launch through Steam.
spellman23
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