I'm a big fan of Favo[u]rites for switching working directory. I have all my current projects there, plus the main ones I need to access for legacy issues, plus my temp directory and RAM drive for Mechanica work.
If you're frequently switching between two projects through the course of the day, you should badger PTC to make their licensing work on a per-machine basis, not a per-instance basis - there are several good reasons to run multiple sessions but at the moment that means grabbing multiple licences, which runs the risk of making you unpopular...