General:
* Inhabit
* Settle
* Occupy
* Dwell
* Live in
* Fill (as in "fill a space")
More specific:
* Colonize (for establishing a settlement in a new territory)
* People (as in "people a city")
* Stock (as in "stock a pond with fish")
* Populate (specifically for data - like "populate a database")
The best synonym will depend on the specific meaning you want to convey.