Joelle --
We based out of Basel with my parents and have done side-trips in the area when our son was 2 1/2 (two seperate trips).
In Basel -- When are you going? They have several festivals that are kid-appropriate: Fasnacht is late Feb/ early March, Herbstmesse in the fall. Jean Tinguely Musuem -- sculptor who makes moving metal sculpture, kids can push the button and see what it does, and what noise it makes... Puppenhausmusuem (doll house musuem) -- has more than doll houses, more of a toy musuem.
Also -- Paper Mill Musuem. Fasnacht-Brunnen. The city trams themselves. Motorless ferry accross the Rhein.
Freiburg, Germany -- very do-able from there. Old town is quaint, unique 'gutters' line the streets, and there is a gondola that runs to the top of the small mountain on the edge of town. We like the restaurant at the top (more for the view than the food) This is a college town, so it is heavy on street performers -- good ones. Our little one loved it.
Interlaken, Switzerland -- Most people stay in the Berner Oberland to see it, but a trip to the Schilthorn is do-able as a side trip.
I feel like I'm forgetting something great for little ones... maybe I'll think of it later.