Assuming you're using the default tileset, is it best to use the smaller houses/buildings, or the larger ones, irregardless of map size? The default house size used in the sample maps program were the smaller houses.Depends.
o What is the size of the map?
o How large is the interior space?
o What is the "tone" of your game? (playful or serious?)
o Are you using default 32x32 characters?
If you're doing a playful kidsy game with 32x32 characters and small maps, the little one is effective.
If you're trying for a more serious look, have larger characters, or have large maps, then I'd go with the bigger one.
I just wonder how out-of-place taller houses look against the default chibi sprites and the default tree tiles. In most cases, 1 level houses that are two tiles high are taller or as tall as a tree tile, which is unrealistic. Trees irl are taller than houses.I never choose 1 tile high walls, even for the default chibi sprites. For me 1 tile is way too small. Houses are big. But there is still an alternative and that would be making the walls 2 tiles high. A lot of people prefer that. And if you go with more realistic proportions and bigger sprites, you can even make 7 tile high walls. Often houses have a second floor.