Probably the best one for horror/sci-fi type stuff would be The Green Hand on Congress St in Portland. The ladies who work there are great and there is a good selection. For more general "rare" stuff you could try Turner Carlson, also on Congress St. For your basic used book shop there is Yes Books. Can you guess what street it's on? Yup, Congress.
Lewiston/Auburn dosen't have much sadly, and it has one that I can only recommend you stay away from. From a purely personal perspective Artios Books in Auburn is one to avoid. A $40 shrinkwrapped copy of Skeleton Crew that was an "implied" 1/1 that was really a BOMC. I count that as one of my early Lessons Learned.
Thats about it! Hope it helps.