My gf's moms water heater pilot light went out this weekend and I can't get it to relight. It's an AO Smith 40gal. gas water heater. I replaced the thermocouple  with a new one, checked the pilot light tube for any clogs and opened the gas line to verify gas flow. It flashes when you push the ignitor, but won't light. I'm not sure what to check next? Any thoughts?

Lower the thermostat all the way down or shutoff power to it for 10 mins,. Some furnaces have a fail safe where if they fail the ignition sequence 3 times in a row, it won't allow it to light until it's been reset. It's possible the gas was off for a short time and caused a fail to ignite. Happened in one of my rentals.

Try lighting with a lighter?

Use a long match to light the pilot, keep holding the pilot valve down until the thermocouple heats up.

I'll try manually lighting it when I get home. The ignitor is working though. Is it possible the thermostat would cause it to not work?

I'm having a similar problem. I have a State Select model. No pilot when I checked. Turned thermostat down to Low or LIght Pilot setting and switched gas to pilot light.
Hit ingnitor and saw spark and light catch. Turned up thermostat and heard burner ignite and start to heat water. Went to bed. Woke up, lukewarm water and no pilot light.
Turned off all the gas and went to the beach for the weekend.

Think mine could be a ventilation issue,,  Saw on diagram that there is a air intake screen/filter on the bottom front but couldn't get down there to see it because of access. Took a skinny brush and brushed blindly underneath there before I lit the pilot. Don't know if that is the issue but it was dirty/dusty as shit under there.

I had a room heater with one of those little push button igniters that I never could get to actually ignite the flame, despite seeing a spark just from it to the pilot.  I always had to use a long match.  You may also want to preheat the thermocoupler and pilot head with the match before as well.  I don't think it would be the thermostat.  Could it be trash in the gas pipe reducing flow?