Best Practices

I generally package with out an exclusion list. (So many sites its hard to keep it up to date for them all, and most of the stuff now is already an MSI so no captures, lucky I learnt what to exclude before App-V became hugely popular)

When training, I train with no exclusion list (how else will they learn??)

Since there is no specific answer... this is how I cover it.

Are the files you looking at, wondering if you can excluded them.
in a folder like %Appdata%\Microsoft??

If yes,
are you packaging a Microsoft application??
if No, get rid.

This is a lot harder for registry keys, but lots more fun too. The same rules apply (generally)

Another tip, you should have clean machines to package and test on. Get to the clean machine, see if the files or reg keys are there, if they are present on a clean machine, you don't need them in your package.

You can also use the conflict mgmt in AdminStudio. Take an OS snapshot and test your MSI against that. Please understand, that is a guide (I last used this for clean ups in about 2006).

Try not to delete things too willy nilly, read up and find out what they are. After a while you get to know most of the files and reg keys on the computer.

Also, I am sure you do this, but make lots of notes and practise installs BEFORE you do the capture, make the least amount of clicks and unecessary actions when doing the capture.
The less you do, the less noise you have to remove.