+1 on Wiswell's post which pretty much covers it. She's been to more of the Madison LBS's than I have, and her comments jibe with my experiences and the LBS reputations that I'm aware of.

The one thing I'd add: Trek's west side store does have that "family/recreation" orientation. (One perk is your little kids can entertain themselves at the store's play table, depending on their ages.) Trek's other store on the east side caters more to serious cyclists.

Also, discounts: some Madison LBS's offer discounts to Bike Federation of Wisconsin members. The BFW website lists Yellow Jersey and Budget, though I thought others did too. Trek stores give a 10% discount to Princeton Club members.