Pretty much what green granite says in his last post.....use this as an educational excercise ....
Other than that, green granite's recommendation of not copying .dll , .exe , or .ini files is a good one. I would extend that list to include .COM; .BAT; .CMD; .VBS; .VBE; .
JS ; .WSF; .WSH . You may need to toggle the "hide extensions for known file types" option in Folder Options (Tools -> Folder Options ->View ... in XP).
You should certainly not copy anything from "C: \WINDOWS" (or %windir%), nor any of your existing software from "C: \Program Files" (%programfiles%) or elsewhere.
And before you put ANY of your old files onto your freshly built PC, make sure you've installed all the latest patches, as well as as anti-virus and anti-spam and other items as per security advice linked to above.
Yes it's boring, yes it's like watching paint dry ..... but you'll feel a lot safer in the knowledge that some gastly individual is not collecting your credit card details and passwords whenever you're online.
As part of your educational curriculum, a brief article from Microsoft on Rootkits...
Rootkits: The Obscure Hacker Attack