user2249: Are there any general guidelines to choose the square colour for your own pawns in bishop endgames? 
Especially in knight vs bishop endgames, would you put your pawns on same coloured squares as the opponent's bishop?

user-1: In general, the pawns should be on the opposite colour of the bishop, especially if this forces the opponent's pawns onto the same colour as the bishop.
This prevents the bishop from being bad (locked in by it's own pawns) and gives the bishop targets.
In my answer to When and why should I trade minor pieces?, I gave this sample position of a bishop dominating the knight:
[FEN "8/8/1k3b2/1p3p1p/pPp2P2/P1P3P1/8/1N2K3 w - - 0 1"]
[Site ""]
[White "Onoprienko"]
[Black "Khasangatin"]


  1. Kd2            Kc6           
  2. Ke2            Kd5           
  3. Ke3            Bg7           
  4. Kf3            Bh8           
  5. Ke3            Bg7           
  6. Kf3            Bf6           
  7. Ke3            h4            
  8. gxh4           Bxh4          
  9. Kf3            Bf6           
 10. Ke3            Ke6           
 11. Kf3            Kf7           
 12. Kg3            Kg6           
 13. Kh3            Kh5           
 14. Kg3            Be7           
 15. Kh3            Bh4           
 16. Nd2            Be1           
 17. Nb1            Bf2           
 18. Kg2            Be3           
 19. Kf3            Bc1           
 20. Kg3            Kg6           
 0-1

This position is cited from Understanding Chess Endgames by John Nunn

user11245: The normal pawn square color rule says: put your pawns on the opposite color. But there's an exception.
So, the precise answer depends on two things:

Are you playing, or are you trying to transition to, an opposite-colored bishops endgame?
If so, and you are the attacker, you follow the normal pawn square color rule: put your pawns on the opposite color.
If so, and you are the defender, put your pawns on the same color as your bishop, so they cannot be attacked by your opponent's bishop, and you can defend them with yours.
If not, then follow the normal pawn square color rule (see #2).

See my response to the question When should I trade into opposite-colored bishops? for more details.

user1485: I mostly agree with the other answers, but want to make one distinction.
Yes, for long-term strategic reasons it is generally correct to fix the opponent's pawns on the same colour as their bishop in order to restrict that bishop.
However, for short-term tactical reasons the opposite is often true. You may want to fix some of the opponent's pawns on the opposite colour of the bishop so that they cannot be defended by the bishop.
Example:
[Title "White to move"] 
[FEN "8/pkp5/1p6/5bp1/8/1P4P1/PK1N4/8 w - - 0 1"]

 1. g4!

White to move plays 1. g4! and black has no way to defend the pawn on g5, with a draw as the likely result.

2249: <p>Are there any general guidelines to choose the square colour for your own pawns in bishop endgames? </p>

<p>Especially in knight vs bishop endgames, would you put your pawns on same coloured squares as the opponent's bishop?</p>
 -1: <p><em>In general</em>, the pawns should be on the <strong>opposite colour</strong> of the bishop, especially if this forces the <strong>opponent's pawns onto the same colour</strong> as the bishop.</p>

<p>This prevents the bishop from being bad (locked in by it's own pawns) and gives the bishop targets.</p>

<p>In my answer to <a href="https://chess.stackexchange.com/a/15231/1108">When and why should I trade minor pieces?</a>, I gave this sample position of a bishop dominating the knight:</p>

<pre><code>[FEN "8/8/1k3b2/1p3p1p/pPp2P2/P1P3P1/8/1N2K3 w - - 0 1"]
[Site ""]
[White "Onoprienko"]
[Black "Khasangatin"]


  1. Kd2            Kc6           
  2. Ke2            Kd5           
  3. Ke3            Bg7           
  4. Kf3            Bh8           
  5. Ke3            Bg7           
  6. Kf3            Bf6           
  7. Ke3            h4            
  8. gxh4           Bxh4          
  9. Kf3            Bf6           
 10. Ke3            Ke6           
 11. Kf3            Kf7           
 12. Kg3            Kg6           
 13. Kh3            Kh5           
 14. Kg3            Be7           
 15. Kh3            Bh4           
 16. Nd2            Be1           
 17. Nb1            Bf2           
 18. Kg2            Be3           
 19. Kf3            Bc1           
 20. Kg3            Kg6           
 0-1
</code></pre>

<p>This position is cited from <em>Understanding Chess Endgames</em> by John Nunn</p>
 11245: <p>The <em>normal pawn square color rule</em> says: <strong>put your pawns on the opposite color</strong>. But there's an exception.</p>

<p>So, the precise answer depends on two things:</p>

<ol>
<li><p>Are you playing, or are you trying to transition to, an opposite-colored bishops endgame?</p></li>
<li><p>If so, and you are the attacker, you follow the <em>normal pawn square color rule</em>: put your pawns on the opposite color.</p></li>
<li><p>If so, and you are the defender, put your pawns on the <strong><em>same color as your bishop</em></strong>, so they cannot be attacked by your opponent's bishop, and you can defend them with yours.</p></li>
<li><p>If not, then follow the <em>normal pawn square color rule</em> (see #2).</p></li>
</ol>

<p>See my response to the question <a href="https://chess.stackexchange.com/questions/15472/when-should-i-trade-into-opposite-colored-bishops/15474#15474"><em>When should I trade into opposite-colored bishops?</em></a> for more details.</p>
 1485: <p>I mostly agree with the other answers, but want to make one distinction.</p>

<p>Yes, for long-term <em>strategic</em> reasons it is generally correct to fix the opponent's pawns on the same colour as their bishop in order to restrict that bishop.</p>

<p>However, for short-term <em>tactical</em> reasons the opposite is often true. You may want to fix some of the opponent's pawns on the opposite colour of the bishop so that they cannot be defended by the bishop.</p>

<p>Example:</p>

<pre><code>[Title "White to move"] 
[FEN "8/pkp5/1p6/5bp1/8/1P4P1/PK1N4/8 w - - 0 1"]

 1. g4!
</code></pre>

<p>White to move plays <code>1. g4!</code> and black has no way to defend the pawn on <code>g5</code>, with a draw as the likely result.</p>
