I just upgraded the WinDVD4 and while it has a few quirks that have yet to be resolved, ultimately they will continue improving audio and video quality and capabilites.
I'm less interested in audio, but I have read there are some significant audio enhancements. Though there are also some things that need to be worked out.
On the video side there seems to be more control and fine tuning available. The PQ looks great to me, then again most flicks on v3 did too.
If all you want is the remote, it will work with v3 (which is what I originally bought it for). I have changed my remote situation recently (TiVo has arrived) and would part with my WinDVD Remote and USB receiver box for $15 shipped.