I had pocket 9's. It was folded around to me at a $.10/.25 table. I raised it to .50, BB called, and here's the hand.

***** Hand History for Game 3320086591 *****
$25 NL Texas Hold'em - Thursday, January 05, 17:42:58 EDT 2006
Table Table 80439 (6 max) (Real Money)
Seat 2 is the button
Total number of players : 6
Seat 1: Matroskin66 ( $27.83 )
Seat 2: woolfyb ( $27.50 )
Seat 4: makuro ( $26.13 )
Seat 5: fladdermusen ( $23.10 )
Seat 6: Edard ( $8.95 )
Seat 3: johnnyBuz ( $35.79 )
johnnyBuz posts small blind [$0.10].
makuro posts big blind [$0.25].
** Dealing down cards **
Dealt to johnnyBuz [ 9s 9c ]
fladdermusen folds.
Edard folds.
Matroskin66 folds.
woolfyb folds.
johnnyBuz raises [$0.40].
makuro calls [$0.25].
** Dealing Flop ** [ 5h, 9d, 3d ]
johnnyBuz checks.
makuro bets [$0.50].
johnnyBuz calls [$0.50].
** Dealing Turn ** [ Jd ]
johnnyBuz bets [$1].
makuro calls [$1].
** Dealing River ** [ Th ]
johnnyBuz bets [$5].
makuro calls [$5].
johnnyBuz shows [ 9s, 9c ] three of a kind, nines.
makuro doesn't show [ Tc, 5c ] two pairs, tens and fives.
johnnyBuz wins $13.30 from the main pot with three of a kind, nines.

If I bet the flop, I am almost positive he would have folded his pair of 5s with 10 kicker. The turn gave him 2 pair, I should have bet more then $1 there right? Something in the 2-3 range to gauge where he was at? I didn't put him on the flush draw so I was thinking maybe 2 pair or an overpair. How much more do you think I could have won here?