I stuck with the unique file number system until I found myself with too many images from too many different cameras and it simply became overwhelming. Now I use a date and jobcode based system instead.
I have Downloader Pro automatically download my files to date-and-jobcode folders — e.g., /060930 AYSA15g for tomorrow's U-15 girls' soccer match — and auto-rename the files similarly. (It also automatically and simultaneously backs up the download to a second external drive, BTW.)
Then (using BreezeBrowser Pro) I cull the shoot down to keepers and rename them in numerical order, in order of timestamp (because I'm frequently using more than one body), so they end up in time order with filenames like 060930-AYSA15g-001.cr2. Then I proceed with processing, web gallery generation, etc. from there.
This way I end up with unique filenames that are meaningful and completely independent of which camera was used. Since I occasionally get print orders from two- and three-year-old shoots, this has proved to be extremely helpful.