Hi,
[27-Apr-2011 19:15:25] PHP Deprecated: Assigning the return value of new by reference is deprecated in /usr/share/php/MDB2.php on line 2647
This is an error message from the PEAR MDB2 package not from Roundcube itself.
Roundcube seems to use PEAR MDB2 package for database connectivity. The current stable release of MDB2 uses assignments by reference (=& new ). There is a newer beta of the MDB2 package available where changelog says dropped php4 support and php5.3 fixes. It can be installed by shell command "pear upgrade MDB2-beta" or you can grab it from http://pear.php.net/package/MDB2/download/
--Martin