My site is reaching CPU limits all the time, I just ran Debug Queries and got more than 4000 queries, no wonder site is slow, I've uploaded the list of queries to http://bit.ly/kPyyu1, would appreciate if someone can take a look at it and maybe tell what I need to do to fix this, I think this should be the problem with the site.
I would bet my bottom $ that the permalinks are the problem, your link shows a heck of a lot wp_rewrite queries.. take a look at this a similar issue
Standard permalink advice is to not start with postnames, tags, categories or authors:
From the Codex on Permalinks
How many pages do you have? Pages.. not posts.
I'd have the same problem in the past with a site with a LOT of pages.
It's even documented as a bug.
If it is your case, try setting $use_verbose_page_rules to false in the WP_rewrite class
Edit: Class WP_Rewrite bool $use_verbose_page_rules = true Whether to write every mod_rewrite rule for WordPress pages.
since: 2.5.0 access: public
To change it, try (not tested):
Anyway, this is a hack. You should read this.