Clean install, backup, recover individual files and applications.

I'm sure this has already been discussed and explained but I'm not quite sure what to look for exactly. If someone can give me a link to the correct thread, that would be fine.
I've had my MacBook for about three weeks now and I never did a clean/fresh install (didn't know that would save a lot of space on the HD). I want to do one now, but how do I go about this?
Sure, first I'll need a backup program (SuperDuper has been reccommended a lot). But what I don't know is whether or not I can choose which files and applications I'd like to put back on the MacBook after the clean installation. I mean, I don't want to recover the entire backup because that would defeat the purpose of a clean installation right?
Also, can I just recover the systems settings separately too?
Yeah, so I hope this makes sense. If not, I'd be glad to elaborate.
Billy
Ps: and what about merely recovering iTunes' library, playlists and such?

One final question: I'm now using my iPod (5G, 60GB) as a bootable HD. Will this corrupt the iPod or harm it in any way? There isn't a real consensus from what I've gathered by swiftly browsing the Internet just now.
Maybe I should've asked this question before starting the SuperDuper procedure
Billy.

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