You can also use FORMAT(X, D) in your query:
Formats the number X to a format like
'#,###,###.##', rounded to D decimal
places, and returns the result as a
string. If D is 0, the result has no
decimal point or fractional part.
mysql> SELECT FORMAT(12332.123456, 4);
-> '12,332.1235'
mysql> SELECT FORMAT(12332.1,4);
-> '12,332.1000'
mysql> SELECT FORMAT(12332.2,0);
-> '12,332'
Edit:
I was about to add that "the downside of using this method is that you cannot that number in your code", but apparently this is not a problem anymore, starting from PHP 5.3, thanks to the parse function of NumberFormatter class:
NumberFormatter::parse numfmt_parse
— Parse a number
Example
<?php
$fmt = new NumberFormatter( 'de_DE', NumberFormatter::DECIMAL );
$num = "1.234.567,891";
echo $fmt->parse($num)."\n";
echo $fmt->parse($num, NumberFormatter::TYPE_INT32)."\n";
?>