I do both, (just to be difficult), with some houses on a small coaster sized base & others that are free standing upon a larger base. To some extent my approach varies according to the building. For example if I want them to have a yard, outbuildings or if I want to put some additional scenery on them. Some houses come with a small built in base too, in which case I usually don't base them.
These are from Timecast & have a small plinth moulded (by TC)around the base. They're freestanding on a larger scenic base.

This is a Scenic Effects church, on its own base with graveyard. The base is a placemat sized piece of MDF.

This is the Airfix ruined farmhouse, on a coaster. I must give it another coat of matt varnish!

A combination of small bases & a larger freestanding base.
