I currently use http://tangorin.com but it doesn't always have the stroke order for the kanji I'm looking up, and better more reliable sites out there?
I dunno, for now I'm just using Jim Breen's EDICT. I'm sure there's something better. If you "examine" a kanji, at the end of its entry, there's a link for "SOD" and "SODA". The SODA is generally better, but either work. But you probably know all this.
The Tagaini Jisho application is based on the same data as KanjiVG, but it features animated stroke orders that you can control. You can also click on radicals, primitives, elements within the kanji itself.