user478: Some programs/websites use 1. ... e5 2.f3 (e.g Arena or LT-PGN-Viewer) while others use 1...e5 2.f3 (e.g chess.com). To achieve this, I loaded a FEN that is black-to-move, then made a move.
Which one is best to use? What does the specs say about this?

Just to make this clear, my question is not about using 3 dots after a white move comment, for this one I got to the conclusion that it is best to use 1.e4 { comment } 1...e5 2.Nf3 over 1.e4 { comment } e5 2.Nf3, but it is somewhat optional.

user291: 1...e5 is best. I quote from Section 8.2.2.2 of the PGN specification, with the relevant phrases in bold:

There are two export format move number indication formats, one for use appearing immediately before a white move element and one for use
  appearing immediately before a black move element.  A white move
  number indication is formed from the integer giving the fullmove
  number with a single period character appended.  A black move number
  indication is formed from the integer giving the fullmove number with
  three period characters appended.
All white move elements have a preceding move number indication.  A
  black move element has a preceding move number indication only in two
  cases: first, if there is intervening annotation or commentary between
  the black move and the previous white move; and second, if there is no
  previous white move in the special case where a game starts from a
  position where Black is the active player.


478: <p>Some programs/websites use <code>1. ... e5 2.f3</code> (e.g <a href="http://www.playwitharena.com/" rel="nofollow">Arena</a> or <a href="http://www.lutanho.net/pgn/pgnviewer.html" rel="nofollow">LT-PGN-Viewer</a>) while others use <code>1...e5 2.f3</code> (e.g <a href="http://chess.com" rel="nofollow">chess.com</a>). To achieve this, I loaded a FEN that is black-to-move, then made a move.</p>

<p>Which one is best to use? What does the specs say about this?</p>

<hr>

<p>Just to make this clear, my question is <em>not</em> about using 3 dots after a white move comment, for this one I got to the conclusion that it is best to use <code>1.e4 { comment } 1...e5 2.Nf3</code> over <code>1.e4 { comment } e5 2.Nf3</code>, but it is somewhat optional.</p>
 291: <p><code>1...e5</code> is best. I quote from Section 8.2.2.2 of <a href="http://www6.chessclub.com/help/PGN-spec" rel="nofollow">the PGN specification</a>, with the relevant phrases in bold:</p>

<blockquote>
  <p>There are two export format move number indication formats, one for use appearing immediately before a white move element and one for use
  appearing immediately before a black move element.  A white move
  number indication is formed from the integer giving the fullmove
  number with a single period character appended.  <strong>A black move number
  indication is formed from the integer giving the fullmove number with
  three period characters appended.</strong></p>
  
  <p>All white move elements have a preceding move number indication.  A
  black move element has a preceding move number indication only in two
  cases: first, if there is intervening annotation or commentary between
  the black move and the previous white move; and second, <strong>if there is no
  previous white move in the special case where a game starts from a
  position where Black is the active player.</strong></p>
</blockquote>
