In my experience a "leftover" I got from previous hacks when upgrading are from the profile/registration pages. If I used any of the custom fields or modified the default ones the settings will be intact...I just reset it when that happens. I believe there is still the Member Field Strip which should resolve any problems you may face with extra profile fields. You can find that in the Members Area downloads.
If you had "Content Enforcer" hack installed you may get an error while upgrading which is pointed to the content_enforcer_adv.cgi file...Just delete it and you're fine. I'm quite positive that since the vars, members and any other folders files (e.g., avatars) are un-touched when upgrading any modifications you did there will have elements of it.
I don't recall running into major problems in any of the upgrades however and so far with my 6.4 testing board (from 6.3.1.1) smooth sailing.
