I started off using
C1 PRO several years ago but they were slow to support Vista when it first came out and I moved to Lightroom.
Lightroom 3 has some nice new features and I'm still playing with it a little.
I recently tried the latest C1 PRO 5 and I liked it but it has one issue that irks the crap out of me. It creates a CaptureOne cache directory (which also has a few sub-directories) in every folder of your library. I don't know about you all, but I like to keep my file system free of clutter. What this also means is that it bloats your directories and will take longer to copy stuff between machines or to removable media.
I would say if you bring yourself to spend $299 or especially $99 through your employer, Lightroom is the way to go.