After doing many reinstalls ( while tweeking ), I've learned to back up the files that are most likely to be changed:
Scenery, Textures, Effects, and any modified CFG's all copied on to CD's.
All my aircraft and add-on scenery are copied on to CD's.
My FSX.cfg, logbook.BIN, GrantedRewards & GrantedRewardsOld.BIN, copied on to CD's.
So If I ever have to do another reinstall (God forbid), I'll clean out the registry, and search for any rouge files, and do a clean install, and put everything back from my CD's. The only pain in the butt, is if you got utillitys that run with the sim (autothumbnail, FSUIPC, ect.) it's best to uninstall them and reinstall from download sites (SimV, Avsim, ect.) so they work properly. So I keep a list of them on an index card with the name of the site I downloaded it from.
FSX is a labor of love, and if it wasn't for the great help and knowledge from this site, I'd still be flying 2004

!