I don't think in my entire poker life, I've had a flopped 2pr from the BB hold up... Should I have folded at any point here...?

PokerStars Game #1649160737: Hold'em No Limit ($0.50/$1.00) - 2005/05/06 - 19:19:12 (ET)
Table 'Aethra' Seat #8 is the button
Seat 1: heat517163 ($100 in chips)
Seat 2: Nightanday ($96.05 in chips)
Seat 3: michton ($84.70 in chips)
Seat 4: Bmxicle ($107.40 in chips)
Seat 5: Pedroboy ($105.10 in chips)
Seat 6: KennyBruin ($46.85 in chips)
Seat 8: fulf76 ($150.65 in chips)
Seat 9: MadRemorse ($111.35 in chips)
MadRemorse: posts small blind $0.50
heat517163: posts big blind $1
Surrey: sits out
*** HOLE CARDS ***
Dealt to heat517163 [Qs 8h]
Nightanday: folds
michton: folds
Bmxicle: folds
Pedroboy: calls $1
KennyBruin: folds
fulf76: folds
MadRemorse: calls $0.50
heat517163: checks
*** FLOP *** [Qd 8c 6c]
MadRemorse: checks
heat517163: bets $4
Pedroboy: calls $4
MadRemorse: folds
*** TURN *** [Qd 8c 6c]
heat517163: bets $10
Pedroboy: calls $10
*** RIVER *** [Qd 8c 6c As]
heat517163: checks
Pedroboy: bets $11
heat517163: raises $19 to $30
Pedroboy: calls $19
*** SHOW DOWN ***
heat517163: shows [Qs 8h] (two pair, Queens and Eights)
Pedroboy: shows [6s 6d] (three of a kind, Sixes)
Pedroboy collected $88 from pot
*** SUMMARY ***
Total pot $91 | Rake $3
Board [Qd 8c 6c As Jh]
Seat 1: heat517163 (big blind) showed [Qs 8h] and lost with two pair, Queens and Eights
Seat 2: Nightanday folded before Flop (didn't bet)
Seat 3: michton folded before Flop (didn't bet)
Seat 4: Bmxicle folded before Flop (didn't bet)
Seat 5: Pedroboy showed [6s 6d] and won ($88) with three of a kind, Sixes
Seat 6: KennyBruin folded before Flop (didn't bet)
Seat 8: fulf76 (button) folded before Flop (didn't bet)
Seat 9: MadRemorse (small blind) folded on the Flop

He played it pretty badly, but why the river check raise? Theres way too much chance he had QJ or AQ for that check raise.

Why he didnt reraise all in, I dont know but I wouldve

Yeah, it seems like a lot of my junk 2 pairs never hold, esp. bottom 2

I wouldn't have checkraised at the end here, I don't think there are many hands he would value bet on the river if he has been calling you the whole way.