Saachez is hard to beat although...Viscous from Cowboy Bebop was pretty darn nasty also.

My top 10 villians of anime from 2000-now have to be these guys/gals:

1) Viscous
2) Light Yagami
3) Dante (Full Metal Alchemist)
4) Gouda (GITS SAC 2nd Gig)
5) Saachez (Gundam 00)
6) Charles zi Britannia
7) Lucy (Elfen Lied)
8) Incognito (from Hellsing TV series)
9) Lil Slugger (from Paranoia Agent)
10) Enderles Kudza (from Trinity Blood)