1) Island in rainbow lake... been trying to find a rune there for siege, but no luck. Wanted a house on that island for literally 13 years, even though its small.
2) House in the Wind mountain passes. Also small but a neat little area.
3) I always liked the vesper cemetary spot. I had a house there once, but it was just too small.
Sadly most of the neat really spots are only for tiny houses. Its not in tram, but other than the rainbow lake spot the abyss house would be my number one pick. Actually id probably pick that first. Not only are they unique, but they are big, and very useful.
I do have a house on the wall in zento, which I dont think I would ever give up.