My wife and I spent ten nights at Hotel Odysseas in the Vlamaris part of Old Samos town in September 2011. We found the hotel to be in a nice quiet area with lovely views over the bay from its terrace. Our room with a balcony, though simple, was adequately equipped and with A/C. Breakfasts were again simple but of excellent quality, the bread so fresh it was still warm, the yoghurt the best I have experienced in Greece, must be about 1000kcal a helping.
If you are looking for somewhere traditional, clean and hospitable, this could meet your wishes.