When running WordPress on PHP5, I receive a bunch of warnings at the top of every page regarding set_magic_quotes_runtime() and 'assign by reference' being deprecated in PHP5. All of these warnings come from wp-settings.php (lines 18, 646, 654, 661, 668, 675, and 711).
The fix is pretty simple, I comment out line 18 (which is the call to set_magic_quotes_runtime) - and I change all "=&" to just "=" for remaining lines, and everything works great.
Any chance WordPress can adopt a similar change (although, likely conditional based on the PHP version)?