Clean install and then restoring just what is needed

I have a machine running SL. It is fine as far as SL is concerned.
Back in time I started out with Panther on a 12" PB. I upgraded hardware and software a few times. As my profile shows I have a MBP 17" with the latest OS.
I had a hard drive fail last Christmas. Apple was great and they replaced the drive. As I was in the US and the backup was in the UK I used the machine for about 2 weeks before I could attempt to restore files. When I got back I found that the account set up did not match so the restore was not clean.
In any event I likely have some legacy files or other junk kicking around that I do not need. Some of it will be outside the user part of the filesystem (old apps, old library files for apps that were deleted long ago).
I had a number of application crashes over the last year running Leopardi. When in at the Apple store to get a fan replaced the Genius suggested that it might be time to think about a clean install. After I told him that I have had a number of system crashes he definitely suggested it was time for a clean install.
Basic model is back everything up and then install from the factory issued disk. Once I have a clean system on the computer I can bring across my files.
Question: How do I get only the files I need or want and not some of the old junk? Frankly I have no idea just what things I need or want in terms of legacy system files. I am pretty sure that everything in my home direction and down from there will be wanted. There will be some apps that I no longer need but how to make sure I am deleting all the associated files is unclear.
I have lots of spare disc space on external drives so I can make a Carbon Copy of the system and a Time Machine back up on a different drive. I am confident of my ability to follow the process once someone can explain what will consistently work. The time involved is not a concern.
Suggestions?

Mac OS X doesn't have a clean install per se.
However, making two bootable clones should allow you room to erase and install Snow Leopard, and just migrate over user data from specific user data folders.
You may have to reregister your licenses for licensed software to avoid issues.
See these two resources to make sure your applications either need Snow Leopard, and/or are Snow Leopard compatible:
http://snowleopard.wikidot.com/
http://www.macintouch.com/specialreports/snowleopard/slcompat.html
and make sure your printers and scanners are Snow Leopard compatible with their drivers:
http://support.apple.com/kb/HT3669
Once that's all the case, then you can migrate your user data from the specific folders on your backup*:
http://www.macmaps.com/safetodeleteormove.html
- * Links to my pages may give me compensation.

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