user7219: I've seen two formats of [%eval] syntax in PGN:

[%eval 250,5] meaning white is +2.5 pawn up at depth 5
[%eval +0.25] means white is 0.25 pawn up

Is any of those mentioned by some PGN standard? Which one is more popular?

user7297: The PGN standard is found here; it does not mention the [%eval] syntax at all. It specifies comments starting with [ and ending with ] but no format for what's inside; that means that program are free to export and import these comments the way they want, without necessarily being compatible.
The only other places where evaluation is mentioned in standard, §13.8 and especially §16.2.5.6, centipawns are used (which would favor the first option):

16.2.5.6: Opcode "ce": centipawn evaluation
The opcode "ce" indicates the evaluation of the indicated position in centipawn units. It takes a single operand, an optionally signed integer that gives an evaluation of the position from the viewpoint of the active player; i.e., the player with the move.

It does not mention the ply depth at all.

7219: <p>I've seen two formats of <code>[%eval]</code> syntax in PGN:</p>

<ul>
<li><code>[%eval 250,5]</code> meaning white is +2.5 pawn up at depth 5</li>
<li><code>[%eval +0.25]</code> means white is 0.25 pawn up</li>
</ul>

<p>Is any of those mentioned by some PGN standard? Which one is more popular?</p>
 7297: <p>The PGN standard is found <a href="http://www.saremba.de/chessgml/standards/pgn/pgn-complete.htm" rel="nofollow noreferrer">here</a>; it does not mention the <code>[%eval]</code> syntax at all. It specifies comments starting with <code>[</code> and ending with <code>]</code> but no format for what's inside; that means that program are free to export and import these comments the way they want, without necessarily being compatible.</p>

<p>The only other places where evaluation is mentioned in standard, §13.8 and especially <a href="http://www.saremba.de/chessgml/standards/pgn/pgn-complete.htm#c16.2.5" rel="nofollow noreferrer">§16.2.5.6</a>, centipawns are used (which would favor the first option):</p>

<blockquote>
  <h3>16.2.5.6: Opcode "ce": centipawn evaluation</h3>
  
  <p>The opcode "ce" indicates the evaluation of the indicated position in centipawn units. It takes a single operand, an optionally signed integer that gives an evaluation of the position from the viewpoint of the active player; i.e., the player with the move.</p>
</blockquote>

<p>It does not mention the ply depth at all.</p>
