I explained that I looked a ways in, but it was too long to read the entire thing.  However, as said thread is linked through many sites, this will at least create a google result for all the people who try to see that problem.  I was here to help people having that problem alone.

I've read the suggestion at http://www.moreawesomethanyou.com/smf/index.php?topic=17746.0;wap2 which explains how to merge files as DBC to make one condensed package which speeds up game speed (and it really does).  However, you may find yourself in the dilemma I found myself in: I had too many mods to merge them without memory crashing if I did not save the file after each import automatically.  However, when I did, I found that merging 500 MB of mods somehow ate up 40+ gigs and then I had no space left on my harddrive and it didn't completely finish.  Of course, this is not covered at all in the opening pages of the thread and I wasn't about to dig through 76 pages to see if anyone may have asked a question about it and had it answered.

Well, after searching through every conceivable folder to see where S3PE was saving these files, I finally came across it (and cleared up 221 GB of total space it ate up, I had measured it after previous failures and confusion of what I possibly saved that took up so much space).  Want your hard drive space back?  Here is where I found it on WinDOS Vista: C:/Users/<profile name>/AppData/Local/Temp

The saved files are the ones which are named similar to tmpFD2A.tmp

Take those (and I suggest only those, the first time I did this I deleted my graphics drivers by accident and had to reload them) and delete them.  Voila, your computer is working again.