What is the best CLI tool (preferably Linux based) that will allow concatenating video files, and also compressing them on the client-side for YouTube upload?
My best bet is ffmpeg. It is powerful enough to do what you want.
You can merge 2 video files with this command line:
mencoder -ovc copy -oac copy video1.avi video2.avi -o output.avi
mencoder, transcode and ffmpeg are your friends (amongst others) you could also use vlc in CLI mode (AFAIK uses ffmpeg) or mplayer (mencoder)