Very neat. I tried it on [[C programming language, criticism]] and I think it built the web in very useful and interesting ways. While arguably linking "computer scientist" and "programming language" was a bit excessive, certainly someone with a more tenuous grasp of C would benefit from linking things like "pointer" and "null character" (even if they could never fully get the criticism just from reading Wikipedia), and articles like "High and low level (description)", "Type I and type II errors", and "classic example" (!) either have potential or are already interesting.
Now, the bugs. :) First of all, it seems to do a string search-and-replace for the *first* instance of each string. That's no good: it tried replacing "The '''[[C (programming language)|C programming language]]''' is a very widely used programming language" with "The '''[[C ([[programming language]])|C programming language]]''' is a very widely used programming language" rather than "The '''[[C (programming language)|C programming language]]''' is a very widely used [[programming language]]".
Second, there were a few odd suggestions. It suggested linking "source code" to "[[Source Code|source code]]", for instance, rather than just "[[source code]]". And in the string "''precompiled headers'', a system where declarations are stored in an intermediate format that is quick to parse. Building the precompiled header", it suggested replacement of the second instance of "precompiled header", not the first (presumably confused by the apostrophes -- although in this case the first bug I mentioned canceled this out :P).
All in all, a very neat tool. Here's my diff (I did tweak the output slightly, but these changes were basically all suggested): http://en.wikipedia.org/w/index.php?title=C_programming_language%2C_criticis...