There's a remote registry editor from MS that I think comes in the WM6 SDK (I don't remember which package installed it) or another very simple and free one
here.
Both work over the activesync/WMDC connection and I've tried them both on Vista 64bit so I'm sure they'll work on other windows versions.
Another tool I use is
WinDiff since neither of the free remote registry editors have a compare feature.