There's really no need to do that... MySQL really doesn't care about how much data it stores.
You can attempt a manual clean-up, but you need to understand the data architecture of both WordPress and plugins really well. Say, you find a table in your WordPress database called
wp_something. Is this table used by WordPress or by one of the plugins? If it is a plugin-created table, is it a plugin that's currently used or did it get left behind by a plugin that is no longer used?
If you're still inclined to try, the best way is to export your blog into a WXR file, drop all tables in the WordPress database, rerun WordPress installation, and then import the WXR file. The obvious problem with this approach is that any data that your plugins used to store outside of WordPRess' default data structures will be lost.