Here I type some scenarious and info on how to use wiki.
Study this file LocalSettings.php
Now users can not create accounts, only admin could do that at login page (Special pages/login page). He should not enter password, but only username and email, and then click "sent by email".
Batch remove of bot users
delete from user where user_id>X and user_name not in ('somelegitusername', 'someotherusername', 'anotherone')
Some info on anti-spam http://www.mwusers.com/forums/showthread.php?9796-Batch-delete-users