Good links pages and directories on sites take some work to put together and to maintain. Ditto with curated outbound links in your articles.
In the case of link exchanges, something I don't generally do, it's helpful to have actually looked at and evaluated the pages you're linking to, and to formulate your own anchor text and unique descriptions. Don't use something lifted off the submitting site, and don't use what they submit to you, even if it's good. Editing and writing your own anchors and descriptions is what saves you from serving up a page of dupe content.
I think well-curated, well-organized resource pages, with good descriptions, can be useful to users and can rank. If some of the links are reciprocal, at this stage of the game, probably no harm. Definitely use dofollow links on these. If you can't vouch for the links you've put into a directory page or an article, then you shouldn't have them there. To offer your site visitors a page of nofollowed links is effectively not taking responsibility for your own content. (These links are not the same as comment links, which you didn't put up and you may not want to maintain.)
Hard to say whether taking down a lot of reciprocal links at your end would preemptively solve a problem with Google... ie, if Google were to be bothered by the inbounds you'd received in the exchange. Depends, I would say, on the percentage of inbound links you have that are exchanges, how manipulative the links are in terms of anchor text, etc etc. If there are enough of them to worry about, you might want to see if can get the inbound links taken down. Perhaps you can do an un
link exchange with your linking partners to get things cleaned up. ;)
See some further comments on this thread... How should you handle a link page on a new site in 2012? http://www.webmasterworld.com/google/4422860.htm