My site has outgrown the current "you may also be interested in" automated method of interlink pages. It was linking articles together based on page titles and it was stuck near the bottom of the page, it's gotta go.
The new internal link structure will use actual keywords relevant to the linked page from within the article content, this is both more optimal in keyword text and in location in my opinion.
The problem is the transition from one to the other. Internal link structure will change a great deal in terms of which pages link to which. The move should be an improvement in terms of relevance but a big change like this has been known to do the opposite to site rankings.
I haven't had to make a link structure change on quite the same scale before, do you have any suggestions? Should I have both methods working at the same time for a period? Should I apply the change gradually or all at once?
Contextual linking for SEO can work very well when done in moderation. It runs the risk of being overdone, and, IMO, is better suited to some kinds of sites than to others. I made some comments regarding these points in this discussion, which may interest you for other reasons as well...
It's perfect for a site like Wikipedia or the New York Times, eg, where the linking often comes in to articles at deep levels, and there's no way of structurally anticipating either the articles or the related pages.
If your site isn't an article site, and if your articles aren't directly attracting inbound links, you may well lose rather than gain if you completely rely on contextual linking globally.