Another recommendation for the Moulin Hotel from me - great atmosphere, good food, and their own brewery!

In Fort William I've stayed in the Imperial Hotel (Best Western, inoffensive, great views over Loch Linnhe), Bank Street Lodge (very central hostel, popular with walkers, not a great atmosphere though, wouldn't stay there again) and Farr Cottage Activity Centre (a hostel with a very laid-back atmosphere, just outside Fort William in the suburb of Corpach).