I agree with Bill.  Your disavowed links will still remain in GWT.  You can download your current disavow file here:

https://www.google.com/webmasters/tools/disavow-links-main

Even if you don't have a manual penalty, it's still not a bad idea to do some disavowing if you may have been affected by the Penguin algorithm.  You won't get a message if this is the case.  And, as Bill pointed out, you can't file a reconsideration request unless you have a manual penalty.

I'd download your disavow file, and review it to make sure that it contains obviously spammy links.  One area that is grey are directory links.  If the company has disavowed directory links that are from non-spammy looking directories it might be a good idea to re-allow them.

Another iffy area is guest posts.  Right now, guest post links are working really well.  But, I am quite suspicious that the next Penguin update will hit sites hard that have used guest posting extensively as a way to rank higher.  For one of my own sites, I have just disavowed a number of guest posting links and yes, I took a hit in rankings.  But, if I'm right, when Penguin refreshes, my site will come out ok whereas my competitors will be in trouble.

And one final thought....if your rankings drop happened any time around May 20, you may be dealing with a Panda issue and not a disavow problem.

Back to your disavow file....if you remove the links that you want to start counting again and re-file, then the next time Google crawls those links they will be credited back to your site again.

The Google quality guidelines say that "excessive" creation of partner pages for the purpose of cross linking is against the guidelines.  But, they don't tell us what constitutes excessive.

This is not always a bad idea.  Here are some criteria I would use to make this decision:

-Would having a page like this actually be good for your readers/clients to use?  Or does it just exist for search engines.  For example, if you are a realtor, having a resource page to list local home inspectors, mortgage brokers, etc. is a good idea and being listed on their resource pages is probably ok. But, if that page contained mostly links to realtors in other cities and unrelated businesses like local casinos or payday loans companies or car insurance businesses then you'd start to think that this page was created just for links.

-What is the quality like on the pages that are linking to you?  Do they look like they were set up just for links?

-Avoid using exact match anchor text.  If your resource page contains links to Realtor in Seattle and Best Home Inspector in New York then that's a sign that it's set up for SEO purposes.

This is exactly the type of link that I spend my days removing for penalized sites.  Don't do it!