WH40K Dawn of War is currently the best of the new RTS's on the market Imo. Looking at Winter Assault (DoW expansion pack) and Tiberium Wars, there is obviously going to be tremendous pressure on modding standards. While I doubt that this will discourage "light" modding (think simple Rules.ini mods from TS days), and though modding skill will likely increase as technology does too, this puts the number of truly innovative and professional-looking mods in a stranglehold.
There has been a disturbingly large number of remake mods as the community passed from TD, TS to RA2 to Generals, and soon to TT (read Tiberium Wars). I do not know of any TS 'total conversion' mods, PPM might barely count. With increased tools for modders, including Will's lovable Voxel Editor, a true scene for modding took off. Those of you may remember the original giants: Federation Studios, where I know AR2 was hosted in its early days; Eclipse. Blitz1, AR2, WH40K, Imperial Assault, Real War, and others.
In Generals/ZH, there are very distinctive and high-quality mods: Halogen, Blitz2, the StarCraft mod, TSR, RAR, even Tower Defense. But as the actual game has become more complex (and formidable to new modders), new mod material seems to diminish. While the mods listed are certainly well-made, I cannot say that they are entirely as innovative as the best RA2 mods.
This is not to say that there can't be any more good mods. However bold things must be done now. Good models and skins and graphics, while of course essential, seem to be overemphasised, while the gameplay and design are all too mundane. But to match the detail of a game like DoW or what I hope C&C3 will be is, at best, formidable. On top of that, fresh, new gameplay ideas are not the easiest things to come up with. In a way, the C&C modding community, as does C&C itself, needs a revitalization.