I am just getting started mining.. which alt-coins have the best long term potential? and which alt-coins over the overall most profitable to mine?
Look for coins that offer something different rather than just being a "me too" clone. Some examples are TAG which has a rewards infrastructure that may or may not catch on, WDC which has some interesting ideas floated including direct USD/WDC "banking" etc. Mining isn't cheap, so ask yourself what it is about the coin that you choose to mine that would compel someone else to buy it from you once mined.
IMHO avoid anything that looks like the devs took a clone of some Scrypt code and added a pretty logo to it. They can be fun to direct your rigs at once in a while when they go bananas on the exchanges, but they're not a solid long term proposition.
As to which are the most profitable to mine at any given time, a site like CoinWarz.com will give you some idea. However: coins at the top of the list very rarely stay there for long, so you may be chasing coins that have already had their moment in the sun for a while.