Quick article on Optimizing your Typo MySQL database, does take a bit and only works on MyISAM and BDB Tables.

mysql -u root
use mytypo_db;
show tables;

Now the beef;

optimize table articles_tags, blacklist_patterns, blogs, categories, categorizations, contents, feedback, notifications, page_caches, pings, redirects, resources, schema_info, sessions, sidebars, sitealizer, tags, text_filters, triggers, users;

Does take a while but should clean up your Typo 4.1.1 Database Tables.