In PHP3, that's about what you can do to release memory.
One question, are keeping big arrays in memory while doing multilevel searches? That is one case in which I've seen "out of memory" problems w/ PHP and MySQL.
Also, to make sure that the problem is not happening at the MySQL server end. Try doing the same SQL queries directly to the server, perhaps using the mysql program.
You should consider migrating to PHP4 and take advantage also of the speed up you get from using the Zend Optimizer (free) w/ it.
I recommend reading the articles:
http://www.zend.com/zend/art/ref-count.php
and
http://www.zend.com/zend/art/under-php4-hood.php
which explain the differences a little more.
Of course the source code will tell you exactly how things are done.
Good luck