We really enjoyed our stay at Pensions Livadoros. We stayed 4 nights and the free transfer from the port was really handy on arrival.
The place is a great little hotel if you're travelling on a budget - the local bus stop at the top of the hill (a bit of a walk in the heat) will get you everywhere you need to see. The pool and room was great and Maria was really helpful with giving hints and tips about making the most of your time in Santorini.
Our top tip would be to hire a quad bike for your stay - it's an inexpensive way to see the whole island at your leisure (we went end-to-end across two days) and cancels out the only downside of staying at Livadoros - it's at the bottom of a hill!