Hi, first of all I want to learn how to calculate my EV in any particular hand, I chose this hand because it has all sorts of betting and raising going on every street.

I am highlighted in red thus ninjawisdom.

PokerStars Hand #73882736866: Hold'em Limit ($0.02/$0.04 USD) - 2012/01/15 14:09:04 CET [2012/01/15 8:09:04 ET]
Table 'Numidia III' 10-max Seat #1 is the button
Seat 1: ninjawisdom ($1.69 in chips)
Seat 2: crazybmv ($0.19 in chips)
Seat 3: Malibu Key ($0.54 in chips)
Seat 4: Allex315 ($0.33 in chips)
Seat 5: Bushlanov ($0.33 in chips)
Seat 6: Capt36Feet ($1.97 in chips)
Seat 7: SerJoker79 ($0.93 in chips)
Seat 8: skytreker ($0.89 in chips)
Seat 9: tupesis123 ($1.39 in chips)
Seat 10: gyusco29 ($0.69 in chips)
crazybmv: posts small blind $0.01
Malibu Key: posts big blind $0.02
*** HOLE CARDS ***
Dealt to ninjawisdom [9d 9c]
Allex315: folds
Bushlanov: folds
Capt36Feet: folds
SerJoker79: calls $0.02
skytreker: folds
tupesis123: folds
gyusco29: folds
ninjawisdom: raises $0.02 to $0.04
crazybmv: folds
Malibu Key: calls $0.02
SerJoker79: calls $0.02
*** FLOP *** [Tc 4c Td]
Malibu Key: checks
SerJoker79: checks
ninjawisdom: bets $0.02
Malibu Key: raises $0.02 to $0.04
SerJoker79: calls $0.04
ninjawisdom: calls $0.02*** TURN *** [Tc 4c Td] [Ac]
Malibu Key: bets $0.04
SerJoker79: calls $0.04
ninjawisdom: calls $0.04
*** RIVER *** [Tc 4c Td Ac] [9h]
Malibu Key: bets $0.04
SerJoker79: raises $0.04 to $0.08
ninjawisdom: raises $0.04 to $0.12
Malibu Key: raises $0.04 to $0.16
Betting is capped
SerJoker79: calls $0.08
ninjawisdom: calls $0.04
*** SHOW DOWN ***
Malibu Key: shows [4s 4h] (a full house, Fours full of Tens)
SerJoker79: mucks hand
ninjawisdom: shows [9d 9c] (a full house, Nines full of Tens)
ninjawisdom collected $0.81 from pot*** SUMMARY ***
Total pot $0.85 | Rake $0.04
Board [Tc 4c Td Ac 9h]
Seat 1: ninjawisdom (button) showed [9d 9c] and won ($0.81) with a full house, Nines full of Tens
Seat 2: crazybmv (small blind) folded before Flop
Seat 3: Malibu Key (big blind) showed [4s 4h] and lost with a full house, Fours full of Tens
Seat 4: Allex315 folded before Flop (didn't bet)
Seat 5: Bushlanov folded before Flop (didn't bet)
Seat 6: Capt36Feet folded before Flop (didn't bet)
Seat 7: SerJoker79 mucked [Kc Jc]
Seat 8: skytreker folded before Flop (didn't bet)
Seat 9: tupesis123 folded before Flop (didn't bet)
Seat 10: gyusco29 folded before Flop (didn't bet)

just go to twodimes and put them in at various points

Download this no cost tool, you can run it for each street to see how effective your decisions were. It is a good learning tool

http://www.pokerstove.com/download/

Your EV is constantly changing throughout the hand. Prior to the river, you don't have much equity (you need to hit a two outer to beat a made full house).
The hand history is difficult to follow, but I think there's 24c in the pot prior to the turn card, then 32c after the other players bet and call. You have to call 4c, so the pot lays 32:4 or 4/36=11%.
If you estimate that you have a 8% chance of hitting a 9 on the river, and you have to contribute 11% of the pot, it's not immediately +EV. However, you have position and can fold on the river when you miss, but could win a bigger pot when you hit and get paid off. Because of the implied odds, the call on the turn makes this a +EV play.
You only had to call 4c on the turn, but ended up winning 85c, which is a huge return on your investment.

twodimes didn`t make much sense to me...

Use Pokerstove or Equilab instead, then.
Enter your hole cards (99) in one box, 44 in another, and "??" or random in the third. Click evaluate and it will tell you your equity pre-flop.
Now enter the flop cards and click Evaluate again. Your equity will have changed. (You are drawing very slim).
Enter the turn card and evaluate again. Notice that you only have 8% equity. That's because you have to hit one of the two remaining 9s in the deck. Prior to the river hitting, you have 8% equity. You compare that with how much money was in the pot, and how much you had to pay to see the river. When the pot lays better odds than the card odds, it's a good call.

thx, pokerstove was too old or something and the newest version is blocked by my firewall or something, I`m gonna take a look at equilab