Does Time Machine backup programs like Photoshop and iWork?
Usually the apps like PhotoShop just come across with all the right licenses.  However, sometimes you must contact the vendor if they have a draconian DRM policy where they are tied to a specific machine / OS.  

I'd be very concerned with Adobe if it was a new machine but I've done the upgrade "in place" for Creative Suite at least twice on my MBP 2010.

To upgrade "in place" I just allow the installer to do its thing, and only keep Time Machine in the loop for catastrophes.  If I'm super paranoid I'll take a disk image onto USB using some program like SuperDuper!