Big Momma's is the name of the Commercial Street coffee house. It is nice. It's on the "nice block" of Commercial Street, just east of Boonville Ave.
My other favorite is The Coffee Ethic. It's new and mod with organic coffees and connected to a new branch of the Springfield public library. Once my partner and I got cruised there which was hilarious! It's on Park Central Square, around the corner from MudHouse (which, though gay-owned and awesome, has a lot of Bible-studiers, bless their hearts, and sometimes I like to skip that crowd).

The MudHouse & MudLounge downtown are gay-owned. While they aren't exclusively gay establishments they are both accepting locations and have mixed clientèle.
I don't know if the Magic Bean has a current incarnation, but it was also a comfortable environment.
GLO used to have a business guide to springfield... though I don't know if anyone has bothered to update it since it was published in the late 90s...
Oh, and there's a coffee shop on Commercial St that I've visited a few times and I know of several people in the neighborhood who frequent it.
Good luck on finding a place that's a good fit for you!