I can't see this causing you problems.  I've commonly noindexed huge numbers of pages, mostly for sites with Panda issues, and in several cases we've seen great increases in traffic with a future Panda refresh.

That's great news that you got the penalty revoked.

It can often take a few days for the manual spam actions viewer to show that there is no longer a penalty.  Also, keep an eye on the manual spam actions viewer.  I've seen a number of sites lately that got a pure spam penalty revoked and then a few days or weeks later got either a thin content penalty or an unnatural links penalty.  Hopefully that's not the case for you though!

There's a lot of stuff written about duplicate content that just isn't true.  John Mueller from Google has said several times that there is no duplicate content penalty.  However, if two pages have the exact same content, Google won't want to show both to the searcher.  They'll pick the most relevant one, or perhaps the one that Google has decided is the originator of the content and show that one.

So, if you have two sites that are identical, most likely one won't rank well.

Some ezine article links are indeed followed.  This can cause problems, because some websites can have, say 9 nofollowed links from ezine article pages and then the 10th is followed.  As such, many people miss those.

That's great that your article marketing didn't hurt you, but this is exactly the type of link that can hurt others in the eyes of Penguin.

Adam, it's good that you got the articles removed.  You may also want to do a search for the text of these articles in case someone has taken them and republished them as these will be unnatural links too.

If you do find additional article links that you can't get removed, just disavow them.  Make sure you do so at the domain level.

If you've got viagra spam pointing at your site you likely won't be able to remove them.  So should you disavow?  Disavowing a nofollowed link won't accomplish anything as disavowing is simply asking Google not to count the link and a nofollow link is already not being counted.  However, when you have loads of nofollowed links from spam attacks this is one situation where I often do go ahead and disavow these.  The reason for this is that one tactic that spammers can use is to point a bunch of nofollowed links at a site and then one day turn them all to followed.  If you've got them disavowed then you've got that covered.

Also, if you have viagra links pointing to your site, make sure you don't have a hack within your site.  Try doing a google search for site:yourdomain.com viagra and see what comes up.

For directories, I don't worry about things like dmoz scrapers and 100searchengines and stuff like that, unless somehow you managed to sneak a keyword anchored link into dmoz.  I wrote a thorough article on my thought process for auditing directory links here:

http://searchenginewatch.com/sew/how-to/2360254/is-that-directory-link-unnatural