I'm sure I've been penalised for some time now for duplicate content..

Originally I had a .com and .co.uk domain each with the same site, I've now (some time ago) 301 redirected the .com to the .co.uk. However, I've recently come back to this and noticed I've had some .php file and /directory/ url's with the same content in - would google see this a duplicate content too? Needless to say I've 301'd the .php's to the /dirs/

Now, should I send a re-inclusion request to google to get this sorted out, or just let things take their natural course?

It's often difficult to say exactly why a site is banned. Unless you know exactly what you did - eg. hidden text, sneaky redirects, etc.
If you're putting in 301's on your old domain's php files to your new domain, then asking for reinclusion would be asking for trouble. Why ask for reinclusion for a site that redirects to another?

In case you haven't already done so, use Google Sitemap to get your site indexed. Sitemap accounts also have a new form to ask for reinclusion in case you want to do that as well.

Good luck.
-Jeffery

I did that with my site and it was fine (I moved links.php to /links/ ...). I think if you are moving the content to a new location, rather than creating duplicates, Google won't penalize you for it. I would thank that at the worst, they may index the "duplicates" as omitted results but that's just IMO.