Same problem here:

[Wed Aug 08 17:41:48 2012] [error] [client x.x.x.x] PHP Deprecated:  Assigning 
the return value of new by reference is deprecated in /usr/share/php/MDB2.php 
on line 393
[Wed Aug 08 17:41:48 2012] [error] [client x.x.x.x] PHP Deprecated:  Assigning 
the return value of new by reference is deprecated in /usr/share/php/MDB2.php 
on line 2647

precise (12.04), x86_64

$ dpkg -l | grep roundcube
ii  roundcube                        0.7.1-2                         skinnable 
AJAX based webmail solution for IMAP servers - metapackage
ii  roundcube-core                   0.7.1-2                         skinnable 
AJAX based webmail solution for IMAP servers
ii  roundcube-pgsql                  0.7.1-2                         
metapackage providing PostgreSQL dependencies for RoundCube

$ dpkg -l | grep php-mdb2
ii  php-mdb2                         2.5.0b2-1                       PHP PEAR 
module to provide a common API for supported RDBMS
ii  php-mdb2-driver-pgsql            1.5.0b2-1                       PHP PEAR 
module to provide a PostgreSQL driver for MDB2

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https://bugs.launchpad.net/bugs/803299

Title:
  Roundcube logs a lot of 'PHP deprecated' messages

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