What if they just call with a set?

Do we pay them off when the board pairs?

No exact hand histories.

Hand 1. 1st level of Stars $16 SNG. 3 limpers to me with Ac8c in BB.
Flop (pot 80) QT5 2 clubs. I bet 60, 1 limper calls.
Turn 7c (pot 200) completing my flush. I bet 160, limper calls.
River T, pairing the board. (pot 520). I bet 300, limper raised to 750, I called, limper showed 55 for the boat, I was crippled and proceeded to lose the thing.

Hand 2. Live SNG. 4 handed, blinds 2/4, opponent isn't out of line. I raised to 15 UTG with AcKc. BB called.
Flop Q85 all clubs (OMG imagine how I felt). I bet 25, BB check-called.
Turn a red Q. Pot was 80, BB checked, I pushed AI, a slight overbet of 100 or so in total. BB called me with 88.

Here come the obvious questions:
How should I have played these / Was there anything else I could have done?

Well, you had nut flushes in both instances with a set needing to improve to the house to win. I don't think you could have done anything differently in those situations, and even then probably wouldn't have changed the result. Very few people will dump a set, even on a flush board, hoping that they will pair and improve.

Likewise, very few people can dump the nut flush in the face of a board pair, although that is more likely than dumping the set, assuming you can get a good read.

In the first hand, you put your money in when you were ahead, so don't lose any sleep on that hand. Second hand, you got your money in when you were beat. You potentially could have bet out the set with an immediate allin, depending on how tight the player is, but that is unlikely. Otherwise, you could have slowed down a little when the board paired and you were checked to. But, only you know whether you would have had the discipline to lay your nut flush down when shoved to in a paired board.

Bottom line, don't sweat it, it happens, but not often enough for you to change your style of play.