Apparently, it's ok to have more than one version installed. On my beige G3, I've got version 2.5 (for full-screen playback of movies, as well as its many transcoding options), and also whatever QT version was installed with OS9.1. They happily coexist, as far as I can tell. I use 2.5 to convert movies into Cinepak (for playback on 68k machines), and MPEG1 (for lower-end PPCs).
Having only, say, 4.0.3 locks you out of many of these options. As I mentioned in my earlier post, Apple *removed* these features from later free versions.