lower your APC TTL values and it may help with fragmentation
also you may want to consider updating to latest PHP using the DotDeb Repos and/or switching to nginx/php-fpm (which again you can get latest versions via dotdeb)
more info about dotdeb here:
http://www.dotdeb.org/WP-MU only helps reduce APC usage on the global/opcode cache size but is a worthwhile thought
you should also look to set apc.stat = 0 as well if these are the only php sites on here and you have w3tc setup with APC on all sites and running the latest version of w3tc (it will clear apc caches when you update plugins which is needed for apc.stat=0)