What I do may be something you might want to try, maybe as a last resort.
I format my drive into 2 partitions, a C: (30 gigs for Vista, 15 gigs for any other windows) and a D: with all the rest of the hard drive space. The C: partition gives me enough room for Windows, the few apps I install into C:\Program Files, and enough additional space to save pretty much any file on my desktop. The D: drive is where I put everything; 'specially programs. Programs that I have to install get put into D:\ProgNew, programs that can just be unzipped get put into D:\ProgNoInst. After a format pretty much all the programs in ProgNoInst will continue to work as if nothing happened. I'll also change the name of the ProgNew folder to ProgOld. Then I'll go through ProgOld and delete any program that I'm no longer interested in using.
After I install a program that I had installed before I'll use Beyond Compare to compare the New with the Old. If there's file differences, specially in .ini files, I'll selectively transfer the Old stuff to the New stuff.
Sometimes after a format I'll rename the ProgNew folder to ProgKeep. Then I'll try every program I'm still interested in and see if any still work. Any that do I'll leave in the ProgKeep folder for easy future formatting.
The first couple times going through this process takes a little extra time, but after a while I build up a collection of software that I don't need to worry about getting messed up if Windows decides to take a crap on me. I suppose it would be easy enough to backup all the -non-install- programs periodically to help protect against a HDD failure or something.
NixSaver looks like a very good solution for other software that must be installed though. justice, what do you mean by "Opera only" in that table?