Niki's Hotel is cheap and cheerful with good balconies and reasonable breakfast in a good part of the town.
Hotel Isole in a narrow side street to Socrates street, is one of the most charming little hotels I have visited. Just a few rooms ("Sultans suite" with great views over the roof-tops), most floors out of level, high ceilings, originally decorated and close to everything. They serve breakfast, and gives you the best advice for a good taverna for dinner (Greek , not touristic !)
We have just booked Sofia Pension for 3 nights in September
Sofia is in a great location right in the middle of the Old Town. The only down side is you may struggle to get a taxi to take you there - speak to the hotel as most usually have drivers that they know who, depending on time of day, will venture right into the Old Town.
If you can't get right into town via taxi I would suggest you get a taxi to drop you at "San Francisco" Gate and walk in from there - this will reduce the amount of dragging bags uphill you have to do.
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