Okay, here is a game where my opponent made horribly inaccurate move in the first few moves causing structural weakness. The rest of the game was exploiting the weaknesses.

One of my horses got way overworked and the local chapter of PETA made threats.

Online chess, three days per move. Names have been removed to protect the innocent.

And my in-game notes

Move 8

Okay, this has to be a technically won game for White. Now let us prove it.

CM: O-O, Nc3, Be3, Qc3

O-O seems safe enough and I will end up playing it anyway

Move 9

Time to pin the Knight. He is practically forced to defend with Be7 or I am busting up his pawn structure even more.

CM: Bg5, Rd1, Qc3

Hmmmm, If Bg6 does Qd4 work for Black?

Move 11

He makes my life too easy.

CM: Qc3, b3, Bxf6, Qd3

11 Qc3 Nxe4?? 12. Qxf6+ Kf8 13. Bxf8+ and White wins easily 

11. Qc3 O-O 12. Qxe5 Re8 and White has to be very careful.

Move 13

I want to take some space with tempo. a4 seems very good.

Move 14

Are you serious? If I trade Queens, I can mess up his pawn structure even more than it is now.

QxQ seems obvious and I don't see anything else I want to consider.

Why do my moves keep getting lost? ( I think I make my notes on one screen, then go to the other game board and save my notes there, overwriting)

Move 25

CM: b4

Now I just need to find out if it works.

Critical line: 25. b4 Bd6 26. Nc4 Ke8 Rxd6 cxd6

Move 26

Evaluation: White is still better, but I am not seeing the continuation. I have to pull out with the Rook, and have three possibilities. 

Rd3 makes sense. I may want to redeploy my Knight to f6

Move 27

Evaluation: Still a game. Still have advantage

Double rooks? Advance on King's side? Nc4? Nb3? Doubling rooks makes sense except my Knight is pinned to the pawn if he plays Ra6

I like having the Knight on a5 where it puts pressure on c6.

27. Rad1, Ra6 28. g4 c6 and I have some problmes

Move 28

I still have the advantage, but I thought I'd end up winning a pawn.

CM: Rad1,

Move 29

CM: Ke2, RxR, Na5

Move 33

Penetrating with the King after I exchange Rooks.

Move 36

Sitting on his head with Kf5

Move 38

CM: bxc, b4, Nd5

bxc, Kc6

b4, c6

Nd5, cxb, cxb

My preference Nd5 is best follow closely by b4. bxc is inferior.

move 40

(I have significant analysis on paper that I need to type here)

Move 41

Wow, I really though Kd6 was his best try. This move is inferior.

Those PETA bastards...

You should have traded pawns: 

PETA Gave Me Death Threats For This Game

ROFLOL

Agreed. In my annotation on the 5th move I note this: "I decide to go for the weakening of the pawn structure. In hindsight I would have traded pawns in the middle first."

wut is PETA anyway?

You awful, awful man. It was clear that your pony was exhausted! Shame on you.

Good game. I like your title.

I am not sure if you are still monitoring this thread, prfen, but I would like to ask for your thoughts.

As I attempt to improve my game, I have identified two areas of weakness: One, I do not consider pawn advances on the flanks, my incorrect mindset is that they cause weaknesses. The second is that I overvalue the importance of avoiding doubled pawns. I am using online chess and some experimentation to try to correct some of the bad models I have learned.

Are there any good sources to learn more about these topics? What would you recommend?

Buy Pawn Power In Chess by Hans Kmoch. He describes all the major pawn formations. It's a little difficult to find, but I think Amazon might have it.

I am actually familar with that book, thanks for recommending it. If memory servers, though, I don't think it covers the idea of flank attacks with the pawn. Or does it?

qd5!! gives white a huge advantage doesnt it? Qxd5 exd5 Bxf3 gxf3 a6 dxc6 axb5 cxb7 Rb8 a4! and white will get a 3 on 1 majority on the queenside...

black doesnt have better i think, he drops the pawn for basically no comp otherwise?

There is no doubt that white has an advantage. 

White could easily steer the game into a won endgame position, even though the advantage is very slight.

It reminds me of Capablanca in his game against Reti (an endgame genius) who assumed that the position was a draw, but Capablanca at a glance calculated it as a win. 

Those doubled pawns may not seem like anything now, but I promise you that white stands much better.

My knight was quite busy here, but did a good job in the end 

http://www.chess.com/livechess/game?id=485312972

My knight took a beating here: http://www.chess.com/echess/game?id=57702968

I knew the game was drawn, but I wanted to go Magnus-style by probing for weaknesses, and I finally got some, and ended up winning