I noticed a very active super admin that helps users setup their blogs had an excessive amount of usermeta tables. There was over 416,000+ entries that included meta_key's capabilities, user-settings, user-settings-time.
It was causing Fatal Errors and slowed the entire network down. The only way to clean it up was to do a bit of house work on the database. I talked with JJJ about this issue and he mentioned to use DELETE FROM
This helped loading issues and the occasional fatal error memory allowance exceeded. Thanks John!
edit: When I get a chance I will update this post with more information. I currently don't have my notes with me.