would be nice if NMM stored what mods you downloaded to your account, like how Steam stores the games you purchased in your account and allows you to re-download them upon re-installing. That would eliminate the hassle remembering the mods you had and searching for them again... granted if you were just reinstalling NMM to a new directory all you would have to do is point the mods folder directory to the former, or new directory they are in, but if you had performed a system restore or re installed windows then this account bound library of mods downloaded would be of great use. Luckily i made a list of all mods with links before my HDD failed and i had to install on a new HDD, but now my list is almost doubled.
However, in the options, i'm more than certain that you can redirect the NMM to the old directory, go to [Settings] then click (for me it's Skyrim) the [Skyrim] tab and the first directory option is "Mods Directory" hope that helps! 
Thank you pillow for the reply. 
yeah that's what I did before. actually I had to wipe out the system, but I still had NMM as I had installed it on a separate drive. so I didn't have to reinstall it at that time, but i did need to redirect NMM back to the original "mods" and "install info" folder. then I was able to get all the installed mods back, but the problem was all the assigned categories were gone, i.e. all mods were under "unassigned" categories.
So this time, I want to make a backup of all the assigned categories before I move NMM to another folder, just to be safe.
P.S. Personally I dont have a problem with remembering the mods I've downloaded, cuz I always manually download the mods and keep them in a separate folder. Linking all the mods you've downloaded to your account is a good idea, but besides that, in the meantime, i would say an import/export function for category assignment will help a lot.
EDIT: forgot to mention, I tried "reset to nexus site default" when i lost the categories, but it only worked for some of the mods, not all of them.
Edited by x0pht, 22 February 2014 - 06:21 AM.