Time Machine Works, but applications no longer registered

So I finally broke down and bought and external drive yesterday because they were on sale (I've been pining after 1Tb drives for over a year), and quickly went to work backing up all my data with time machine. My Mac had gotten a little slow for whatever reason, but I decided to back up everything through time machine, re-image my hard drive, and bring back in all my documents and apps--these being the only really important things on my laptop. I thought if I re-imaged and got rid of all my excess files, the index would be smaller, and apps would be found and launched a little faster. I also try to keep my HD load pretty sparse--I'm a college senior and bring it to a lot of internship jobs/other jobs/classes, and like it to look not too cluttered.

The issue is that after I went back into Time Machine and "restored" my applications folder, all of my Apps now are either "broken installs" or come up as unregistered apps. I'm also missing all my save-game files and video-playback components for quicktime. I could go shuffle through all my CD's and DVD and enter all of my serial numbers manually, as well as reinstall all of my add-ons and extras, but the whole reason I use Time Machine, rather than fresh install everything to begin with, was to avoid this problem! I'm really hoping there's an easier solution here than manually reopening ALL of my apps and entering the serials--that'll take hours! I also tried using the "migration assistant", no luck there either. Any ideas?