I was starting a session and building the number of tables I play. Just as I was going to click the raise button, PS put another "Do you want to join this table" message in front of me. After I clicked on it, I mis-clicked and only called the bet from the button instead of raising to $0.50 like I planned to.

After swearing profusely, I was a lost in how to play the hand since the villain could have anything at that point and he certainly doesn't have me on a big pair. Help on the flop on through would be appreciated.

Villain was TAGish, not enough data to get more of a read than that. His limp certainly suggested a weak hand, but one the flop could have easily hit. My play at the time would look TAGish as well, but one who abused position when shown weakness (raising limpers late, raising frequently to steal in the CO and BTN position)

BTN ($12.15 in chips)
Hero ($12.05 in chips)
BB ($4.95 in chips)
UTG ($8.40 in chips)
UTG+2 ($9 in chips)
MP1 ($5.65 in chips)
MP2 ($5.15 in chips)
MP3 ($5.05 in chips)
CO ($8.90 in chips)

*** HOLE CARDS ***
Dealt to Hero [A A]

6 Folds, BTN calls $0.10, Idiot Hero calls, BB checks

*** FLOP *** [5 6 9] ($0.30)
Hero checks (my thinking was that I didn't represent much pf and I would c/r instead of donk bet), BB checks, BTN bets $0.20, Hero raises to $0.80 (there weren't any draws to worry about and I wanted to keep the villain in by giving him about 2:1), BB folds, BTN calls

*** TURN *** [5 6 9] [7] ($1.90)
Hero checks (I was unnerved by the 7, because if he had any 8x combination, I was drawing dead. Should I have been?), BTN bets $0.50, Hero calls (I'm getting nearly 4:1 to call and since I showed weakness, he might be trying to cheaply get me off the hand.)

*** RIVER *** [5 6 9 7] [3] ($2.90)
Hero checks (my thinking is all I have is an over pair and will be happy to show this hand down), BTN bets $1.50, Hero ?

I know I'm getting 3:1 and the villain can't suspect I have AA because of how mangled the hand has been played. Yet my gut is telling me he has the straight. Raising seems out of the question, but should I call here?

Your hand is way underrepped, I think you pretty much have to make a crying call. You got to the river very cheaply, so the river decision isn't too costly if you're wrong. Definitely lead that flop, though. No one raised pf, there's no reason to think anyone is betting the flop and giving a free card there is bad.

I reccommend getting stars planner ahk script it will take care of those pesky waiting list pop up boxes for you by accepting the waiting list message, got to lead that flop though. In a limped pot you should want to keep it somewhat small, especially with that flop texture. The checkraise builds the pot to the point where you may have to make some difficult decisions later on when there are a lot of potential scare cards and little chance of your hand improving.