ryanair is great and cheap...sometimes the airports are out of the way, though, and bus/rail/whatever to get into the city you're actually going to can be expensive and inconvenient. always look into that before you book.
2 really great websites:http://www.bahn.de
(click on internat. guests at the top for english) can give you train times/schedules for all over europehttp://urbanlowdown.com
reviews/recommendations/etc written by expats living or studying in europe
i lived abroad for a year and did 2 months straight of backpacking, along w/a couple smaller trips. it's such a great experience! my favorite places were rome, budapest and portugal. portugal is seriously like an overlooked paradise. there weren't too many tourists, it's cheap, and the people are so friendly! if you like port wine, i especially recommend porto, in the north. it's gorgeous and there's a whole neighborhood of wineries (porteries?) where you can wander and drink free port all day.