There really isn't a "best" codec to use for web movies. Everyone has their own preference. Really, the only thing you can do is pick one that works for you and run with it.

I personally use QuickTime movies compressed with either Mpeg4 or Sorenson 3. Mpeg4 is nice, because the preset options usually work pretty well. However, I generally prefer Sorenson 3, because I get much better control over how the data is compressed. All of the movies on my website (see my signature below) were compressed with Sorenson 3 and Mpeg4. I'm happy with how they look.