common 2 pair f-up for me...help!

I frequently think my two pair is the best hand when it isn't. I can't distinguish between the other guy betting with top pair or a better 2 pair than me. How could I have played this hand better?

***** Hand History for Game 2410928980 *****
$25 NL Texas Hold'em - Saturday, July 23, 14:54:09 EDT 2005
Table Table 37028 (6 max) (Real Money)
Seat 2 is the button
Total number of players : 5
Seat 1: visionsplend ( $18.15 )
Seat 2: lugger05 ( $22.95 )
Seat 3: jackasschris ( $11.30 )
Seat 5: CaptnCanada ( $15.35 )
Seat 6: th3fold ( $49.10 )
jackasschris posts small blind [$0.10].
CaptnCanada posts big blind [$0.25].
th3fold posts big blind + dead [$0.35].
** Dealing down cards **
Dealt to th3fold [ 3d 9d ]
th3fold checks.
lugger05 calls [$0.25].
jackasschris calls [$0.15].
CaptnCanada checks.
** Dealing Flop ** [ 3s, Jh, Kh ]
jackasschris checks.
CaptnCanada checks.
th3fold checks.
lugger05 checks.
** Dealing Turn ** [ 9c ]
jackasschris bets [$1].
CaptnCanada folds.
th3fold raises [$2].
lugger05 folds.
jackasschris calls [$1].
** Dealing River ** [ 2s ]
jackasschris bets [$2].
th3fold raises [$6].
jackasschris calls [$4].
th3fold shows [ 3d, 9d ] two pairs, nines and threes.
jackasschris shows [ Jc, 3c ] two pairs, jacks and threes.
jackasschris wins $16.25 from the main pot with two pairs, jacks and threes.

Two pair is a funny hand..

Heres whats up:

If you're the one betting it and someone else is just calling down, its usually good. Just don't get carried away.
In the small stakes NL, it takes a lot for people to raise you on two streets because they are usually passive. It sometimes is a top pair raising you, but when someone starts playing back you need to slow down. Get paranoid, look for monsters, and apply your reads. If some aggresive retard is raising you, its probably nothing to worry about, but if that guy from The Rundown (aka the ROCK) suddenly springs to life youre in shit with a weak two-pair. Try to get a cheap showdown.

A lot of recongnizing when twopair is good is having a feel for the players at your table and just having playing experience under your belt.

Also, I think you played the hand fine. No reason to get carried away and definitely hard to fold to tiny raises like that.