Two games stand out, for me at least, as being odd that they have not been retro-cloned.
As Sanglorian mentioned, there is no 2nd ed D&D. It would seem to me that it wouldn't be that hard to mod one of the 1e clones to have proficiencies, kits, THAC0, and the other bits that differ between the editions. It would certainly be easier to patch an existing clone than redo 2e from scratch.
The second game that is surprising that it is not retro-cloned, is Nightlife, by Stellar Games. It's a simple game engine with a neat hook. At the time it was released, playing a monster in a near-future urban setting was brand new. But somehow gothic-punk became popular while splatterpunk languished. I blame Tim Bradstreet. Since I haven't had access to my books in the eight years I loaned them to a friend--who moved far away thereafter--I have been missing them of late. Nightlife's lack of a retro-clone is a great failing to the retro-clone movement.
I was going to suggest Gamma World, but my assistant reminded me that there have sort of been official versions of that one already...