500 Error Deleting Excess DB tables Created by Excessive Plugin Use

I my site get’s killed once a day due to what Hostgastor describes as:

I’m showing here that you’re queries need to be optimized. Below is an example of one of your queries that was getting killed due to the amount of time it was taking to execute, you’ll notice it’s a huge query:
[ 1328286601 ] [ johanhor_johanmu ] [ 2162627 ] [ 27 ] [ johanhor_johanmu ] [ Query ] [ KILLED ] [ ] [ SELECT t.*, tt.*, tr.object_id FROM wp_56_terms AS t INNER JOIN wp_56_term_taxonomy AS tt ON tt.term_id = t.term_id INNER JOIN wp_56_term_relationships AS tr ON tr.term_taxonomy_id = tt.term_taxonomy_id WHERE tt.taxonomy IN (‘category’, ‘post_tag’, ‘post_format’) AND tr.object_id IN (8222, 8221, 8219, 8216, 8217, 8218, 8220, 8215, 8214, 8213, 8209, 8208, 8207, 8206, 8203, 8202, 8201, 8199, 8198, 8197, 8196, 8194, 8193, …………………………….(this continue for a page long).

This one query is being executed, and killed as it’s taking too long to execute which in turn caused your site to receive the 500 error due to so many hanging PHP processes waiting on these types of queries to complete. Once you optimize your queries you shouldn’t receive these errors anymore. Here is a great resource on how to optimize your queries: http://hackmysql.com/nontech

I have read through the above and am clueless.

I then came across this http://revellian.com/2008/07/14/how-to-clean-wp-options-slow-mysql-queries/

And checked all my database tables under my multi install wordpress site. I have more than 1000 DB tables (I assume; due to excessive plugin use; plugins that i have killed to a few).

I thought why not kill the excessive DBs. But I have no idea what to leave and what to kill.

I hope you van help. Thanks Johan.