hand 1: easy stack off i reckon..it happens
hand 2: easy call for me especially after seeing 3: flush draws hit and he checks turn you don't bet , he bets big on river....same with both hands. I think your straight has his AJ KJ JT 9T beat.
edit: not so sure about the flop bet though would probably have checked behind as missed set , overcards on the board .

hand 3 : I'd have bet the turn , you got the second nut flush draw and if club comes on the river you won't get any value out of him. Checking behind the turn gives him outs to straights, you don't get to semi bluff the flush to get him to fold .When the river comes non club , non queen and him betting pot .....he could be playing any Ace with 75 0, he thinks you missed the flush and thinks his hand is good. I think it turns into a reluctant fold and kick yourself for not betting earlier.