Actually, I use Winrar, but yes, I unzip to separate folders. My method may seem a bit complex to some, but it works for me.
I have a folder for all my zipped DS games that are the clean files. I unzip individual files to that folder, copy the .nds to the "untrimmed" folder, trim it to the "trimmed" folder and store the trimmed file separately in yet another folder called "Unused DS Games". I then delete the unzipped folder containing the original clean file.
I shuffle between about 50 games at any given time between my R4's 2gig microSD and the "unused" folder. Any .sav files go with it.
I also have separate folders for R4 utilities, skins, firmwares, converters, etc. Same goes for my SCminiSD; utilities, GBA games....blah, blah, blah. All of which are contained within a "DS Stuff" folder.
We have somewhere in the vicinity of 8 terabytes of storage among the 7 PC's, USB hard drives and NAS units, not to mention the piles of CDR's and DVD's around here, so it's no big deal to us to fill 'em up with all kinds of crap. Music, apps, games....whatever.
It all makes sense to ME and that's all that really matters. I'm the admin of our home network, so even my older brother (who bought 98% of the stuff) doesn't really know all the data we have stored away. He encourages me to collect up as much goodies as I can, so I do.
Would you believe that in all that storage space, none of it is pron? It's true.....unless my bro put some in his bedroom PC.....I don't mess with that one, other than to have initially set it up.