On the links app, I think you should:

• Display heaps more links per page instead of 2 screenfuls
• Add the "entire thread" and "x comments" links on the Top Links and Random Links views
• Default the comment viewing options to "oldest first", it's weird to have newest first with a design imitating an anonymous board.
• Remove or fix the RSS. This sort of stuff isn't useful:

<title>Link</title>
<link>http://links.secretareaofvipquality.net/link/99</link>

In a RSS reader, it shows up as an entry entitled "Link" that links to the comment thread. It would be much better if it were like

<title>THE BLANKET THAT HAS SLEEVES</title>
<link>http://www.youtube.com/watch?v=2xZp-GLMMJ0</link>

with the link to the comment thread in the description - in general you will want to see the link first, and maybe discuss later, rather than the other way around.

• If I were you I'd remove all the remaining drupal cruft (I think that's what you use, right?): comment viewing options, comment threading mode, users tab on search results, homepage and subject fields in comments. Those things just get in the way of the simple concept.
• Additionally, I'd like a pony.