Flash is probably the most universal web video format. (Just look at YouTube.) I still prefer Quicktime, though.
Windows users will probably prefer WMV, but that is a hassle to encode. (The high end Flip4Mac is not cheap.) I use Quicktime, because I don't believe that Windows users should be exempt from installing the Quicktime Player. (Clearly I have a grumpy attitude! )
Mini 1.25GHz/1 GB/80G160G400G Mac OS X (10.4.6) FCP 5, Aging G4 Digital Audio, 1 GB, 120GB, iPod Nano