Millennium Harvest House -- A good place to stay with the kids, especially in the summer. The Harvest House has a nice swimming pool and lots of nearby green space; it's also next to the Boulder Creek Path and within walking distance of the Crossroads Mall.
Foot of the Mountain Motel -- There's lots of space here where the kids can expend their energy. Across the street is a lovely park with a playground, as well as the Boulder Creek Path.
Boulder Outlook -- At this former "Holidome," kids can use the pool and play inside even when the weather is bad, and the diversions are many (bouldering rocks, game room, dog park).