I've had good luck with Admin Studio's repackager coupled with Install Shield editor.
We use MSI Studio Pro which is from Scriplogic / Quest / Dell. I don't think it does exe files though.
Are you repackaging using these tools or creating your own installer?
Or are you doing snapshotting. (like the old package builder)
What / How would you go about repackaging something like NotePad++, 7zip, etc?
We "tattoo" the registry so we can query against what was installed by LANDesk vs what was installed by the user.
All we would need is to silently install the application and make these registry settings (the tattoo).
All three. Mostly repackaging. I rarely snapshot as it's my "last hope" to repackaging something.
I personally wouldn't repackage notepad++ or 7-zip as I try to use the vendor installers whereever possible. In your scenario though I guess you'd have to use scripts or MST files for everything to add in your registry tagging (what I would do). We thought about tagging for the exact same reason but the idea got canned due to the amount of extra work.
Another option may be to use the "prerequisite - Run additional file" feature. Haven't used it very often myself though.