I recently played a game as black, where white played d4, and after Nf6, played d3- aiming for (and achieving) a stonewall structure with f4 and c3. I have been fairly befudled by this, having no idea what to try as a plan, the knight eventually getting to e5 is a huge pain, and exchanging it only opens up the f file, any advice?

Maybe you can try to keep your knight on b8 and exchange the light-square bishops by Ba6. Bb7 is not really helpfull...

I play this kind of plan as White against the Stonewall.

mmm, i play something similar as white against the dutch, (even though i usually start e4) but as black there are tricky move orders,delaying f4 for sometimes quite a while, I guess casual play can't be afforded though

you have to take advantage of whites slow development i play stonewall

what opening do you usually play as black? there is several ways to meet it.

A quick ne4 followed by f5 will give a generally very drawish position, which most of the time black can be satisfied with. 
If you play the KID or benoni you can be quite comfortable throwing d6 in somewhere taking away the knights square.

Personally I think fianchettoing is the best way of meeting it, just as you would as white in the dutch. The extra tempo they have a white will mean very little in a closed position.

Don't be afraid of Ne5 in the Stonewall.  Just don't play White's game for him.  Don't initiate an exchange on e5, but cover it well, then shift your Nf6 at the appropriate moment and play ...f6.  Timed right, it can not only expel the intruder at e5, but also quickly enable Black to get in ...e6-e5 as a counterstroke with good effect.

Also, the ...g6 lines are good, playing as White does against the Dutch Stonewall, since it is that with colors reversed.  And you can often play both the ...g6 idea and the ...b6, ...Ba6 maneuver to trade the light-squared Bishops.  That's a reasonable goal as White has voluntarily limited the scope of his dark square Bishop, so if he is left with that as one of fewer minor pieces, he will be worse off.

Don't fear any set-up openings.  If any of them were any good, they would be popular at the GM level, and they are not.

I like these two ways of playing against the stonewall set-up-

pellik in your first example white should play 4 f4 not c3. I think your second line is better but the queen can still be active on the kingside.

I had 4.f4 in there in a variation. After Nb4 black is likely collecting the light bishop or else white must develop his knight to a3 after Bf5. Either way, white is not getting his typical play. 

White of course can still play and attack in the second line. His queen can still be active and his pieces are still on the board. But his coordination has been damaged and his attack is not quite so fast. It's about removing the automatic attacks you see from the stonewall set-up and equalizing, but equality is not winning. 

Oh ok i didn't see the f4 move. Yes the bishop is going to be taken but after cxd3 white has a strong pawn centre. I would agree this is not typical stonewall territory but i wouldn't say its bad for white. You cannot expect to play the stonewall main line in every game and stonewall players need to be ready for these lines. Also 2 Bf5 is another anti-stonewall line people use after which white can play c4 and aim to attack the weakened b7 square.

The c file isn't especially useful to white. It just looks to me like black has found his way into what is rapidly becomming a caro or french where he's snagged the light bishop with a knight (usually a good trade). Objectively equal. 

I do not recognise the position as a french I dont play the caro so will take your word for that. The position may be equal but in theory at least white should have a small advantage due to playing these positions more often. 

White only has a few options for using a center like he gets after cxd3. He can passivly hide behind it and hope to use his pieces, or he can push e4-e5 and you get a center that is quite familiar to french and caro players. 

Well i suppose you would be more familiar with the positions but judging by the IM before your name i take it you don't play 1 h4. The point i was trying to make is as a stonewall player if i lost a game to someone who played one of these anti-stonewall systems i would probably say it was not the opening that caused it. I am interested in what line or lines you play against stonewall players.

Unlike the IM, I will attempt to be as very clear as possible in explaining to you in words, why the Stonewall is a good way for you to learn how to play better chess, but it is not ranked among the openings that White should choose in order to retain the initiative of the first move and press agressively for an opening advantage.

The Stonewall is a variation of the Colle System.  The Stonewall's plan of attack for White is very simple and straightforward.  It is an excellent teaching tool for chessplayers that are still learning the rudimentary basics of opening play and what it is all about.  There is a book that is still available on Amazon.com and Barnes & Noble.com for about $5 or less title, "How To Think Ahead In Chess", by Fred Rienfeld and I.A. Horowitz.  It goes into alot of detail in words and some variations about the Stonewall.  The authors actually recommend the Stonewall as the opening you should play as White.  They also recommend that as Black against 1.e4 you should play the Dragon Variation of the Sicilian Defense.  And, against 1.d4 that you should play, as Black, Lasker's Defense.  It is a book that is suitable for players of USCF rating between 1200 and 1600.  On this website and in this topic you are learning that there are anti-Stonewall systems that Black can play, that Mr.  Rienfeld and Horowitz never mention in the book, even though they know of these anti-Stonewall systems.

 I will continue in a bit.

One system I tend to use in bullet and blitz games against the Stonewall is d6 to prevent the knight from getting to e5; if I have already played d5 when the intent to play Stonewall is shown I will play f6 sometimes, which is usually objectively slightly unsound but is worth it, the knight on e5 is worth a rook sometimes.

Way back when I was 1400, I used the stonewall attack to beat an expert. The guy was fuming angry and stormed out of the playing hall when I won:

http://www.chessgames.com/perl/chessgame?gid=1492238

Anyway, having played the stonewall formations for a while, I got a good sense of the weak points. When facing it as black, I prefer to fianchetto kingside and use g6 to support Bf5 to oppose Bd3. White players tend to take on f5, thinking it ruins my pawn structure, but it doesn't help them at all. When facing it as white, I again fianchetto kingside and seek to eventually wreck black's center with a well-timed f3-e4 pawn break. Stonewall players hate it when you dissolve the center that way, as almost always they get the worst end of the resulting positions.