I find it very difficult to see links alongside normal text.

could we possibly have them auto-underlined, or have the color changed?

Link

Not a link

They are pretty subtle. I don't have issues with it, but could understand others having problems with it. Maybe links autobolding would work...

I've noticed that for reasons beyond my understanding, this seems to be most pronounced on computers using older versions of IE.

I'm using firefox 2.0.0.12

If you're a FireFox user, as long as your not on the bleeding edge of Firefox 3 beta 4, you can use the stylish addon to alter and save customized stylesheets for sites. That way, if you want the links to be purple (or whatever) to help you see them, you can create the customized changes and "attach" them to a page for all time. Sort of like Greasemonkey but for styles.