You should ask yourself something before adding the links. What benefit for users do you want to achieve by doing this? You probably want to increase the navigability of your site. Maybe it is better to create an easier way to add links to older articles in form used to submit new ones. Maybe it is possible to add a "one click search for selected text" feature. Maybe you can add a wiki-like functionality that lets users propose link for selected text. You probably want to add links to related articles (generated through tagging system or text mining) below the articles.
Some potential problems with fully automated link adder:
You may need to implement a good word sense disambiguation algorithm to avoid confusing or even irritating the user by placing bad automatic links with regex (or simple substring matching).
As the number of articles is large you do not want to generate the html for extra links on every request, cache it instead.
You need to make a decision on duplicate titles or titles that contain other title as substring (either take longest title or link to most recent article or prefer article from same category).
TLDR version: find alternative solutions that provide desired functionality to the users.