ffmpeg -i INPUT.mov -vf "scale=356:278:flags=spline,unsharp=2.5:2.5:1.5" -b:v 256k OUTPUT.mov
356 is width and
278 is obviously height - replace these with what you need (either can be set to
-1 to keep the aspect ratio).
spline is the scaling method to use, and seemed to work better for me than the default one (full list of scaling methods can be seen here: http://gitorious.org/libswscale/mainline/blobs/master/options.c).
unsharp sharpens the video (I was scaling a video down with this command and sharpening improved the quality of the result.)
Unfortunately there isn't a recipe that'll work for everyone - you will have to experiment to get something good, however this incantation provides a decent starting point.