You don't really need the apple remote to use Front Row (although it is very nice and should still be included with all Macs). Press command+esc to invoke the front row interface and use the arrow keys, enter, and escape to navigate the menus.
I use handbrake (which in turn requires VLC) to rip & convert DVDs to .m4v using the Apple/Universal default and then drag the resulting file(s) into iTunes. Once a video is input into iTunes it will show up in Front Row under "Movies".
Now, for your existing collection you can change .mp4 extensions to .m4v without any processing and then drag in to iTunes.
Most .avi and .mkv will play if you install Perian, but they won't import into iTunes. You can get around this by moving these types of files into the ~/Movies/ folder. You can organize files by folders in this way and Front Row will allow you to navigate as normally. I have noticed some mkv files, e.g. Top Gear in high definition, hiccup at the beginning as apparantly buffering is a bit slow. Probably related to my >4 year old laptop hard drive not being fast enough.
Also, note that you can put an alias in this folder which points to some location elsewhere on your network or collection of eternal hard drives.
Finally, you'll want to use the 'Make Video Tags' script (find it at Doug's Applescripts.com). This is used to force correct video type tagging (and more if you want). While you can adjust tags within iTunes and set flags for Movie, TV Show, Music Video, etc. for some reason Front Row doesn't pick that up and everything gets dumped in Movies. Make Video Tags corrects this problem.
By the way, don't forget to add movie posters and other descriptive details to the tags in iTunes and then they'll be presented just like the movie trailers from Apple through Front Row. Unfortunately cover art and descriptions only seem to work on the primary iTunes library; they do not appear for movies, etc. in shared libraries (check out home sharing in iTunes if you have more than one mac or user account).
Enjoy =)