Hand 1 (400NL). Loose (46/32) villain raises to $16 UTG. Loose passive guy calls in the SB, I make a loose call in the BB with [5h]. Effective stacks $365

Flop $48 [2c][Ad]
Passive guy checks, I lead $28.I thought I'd rep the ace and villain is not likely to have one here. If he calls/raises I am done. I know the bet is small but should be enough to fold out the hands I want to since there are no draws unless someone has a really small SC. Anyway, villain calls, passive guy folds.

Turn $104 Ooohh...not done yet
I check, villain bets $100. I CRAI. Thoughts?

Hand 2 (300NL). I raise to 12 with [Qc] UTG. Villain (38/16) calls OTB. Effective stacks $265

Flop $28 [Tc][Qs]
I bet $15 (small since I don't mind giving a cheap card). Villain raises to $40. I reraise to $120 and plan to call a push. Standard?

#1) Preflop is a big ugly. Post flop is not "fine" as Zmej said. Its beautiful!

#2) I think I would either make a standard CB or check raise the flop. $15 is ok if you plan to reraise if you get raised. So as played I think its fine. Just dont fold once you get raised. Hes probably got something like KT and youre getting it all in, but thats fine.

You forgot the chance that a 38/16 would actually think his 99/88 was best, along with the chances that he has a lower club draw, QJ/JT/J8. Small, but And he folds Kxs. It's a small amount of equity, but $80 in the middle after his raise and the ~$230 behind you. On your range that you're definitely beat right now, 3-betting is +EV.

From Donkifornication's LAGtard Guide to Being Slightly in the Green Over the Last 180 Days to Where Poker Just Might be a Waste of Time- "Ace hi gutshots+FD's+pairs are the nuts."