I don't really give a crap about donuts, they're delicious, but I go kolache every time.
Now, when I say kolache, I'm talking about sausage/jalapeno/cheese. Yes, I like to mix it up occasionally with a fruit/desert kolache, but I don't base my kolache rankings on them. If I do go for a desert kolache, I usually go the cream cheese route though, those are awesome.
The best off the top of my head, based on my experience....
Prasek's Smokehouse in Hillje just south of El Campo on 59
Hruska's on HWY 71 in Ellinger
JR's Smokehouse on 59 about 50 miles SW of Houston
Very good....
Christy's Donuts on West Gray and Montrose in Houston
Snowflake Donuts (Asian owned, Vietnamese I believe) on Webster and Fannin in Downtown Houston (hole in the wall connected to a gas station, looks terrible, but it's very good). They have some croissant kolaches that are really good as well
Good, but way overrated...
Czech Stop in West, TX
The worst....
The Kolache Factory chain, straight garbage. People always bring them in at the office, like they're bring some awesome treats. Freaking ignorants
Aside: Has anyone ever tried "The Original Kolache Shoppe" in Houston? I've never been, but have heard really good things about it. It's down near 610/45 South on Telephone Road.