Why does this site use a darker colour for links that have been clicked on? When scan reading down the pages all I notice are links I've already visited, completely ignoring the pale blue links.
To me this to me seems like a terrible UX.
I've asked a few other people about this and they feel the same way, so I'm assuming it's not just me.
Is there a good reason for it?
The point of visited links is not to make them lighter; it is to demphasize them and make it clear which have been visited.
Remember the default visited link color is purple vs default blue for unvisited for most browsers. It's a bit of a darker color and less eye catching for it; it fades more into the default black text. For many of the early years in web design, purple was almost unanimously the visited link color.
Here's an interesting tip straight from Smashing Magazine: The Definitive Guide To Styling Web Links (emphasis theirs):
Give visited links a darker shade of color, so that they stand out but aren’t as obvious as unvisited links.
Visited Links should be deemphasized and less eye catching. Personally I find UX.stackexchange does this rather well; the darker link color fades more into the black text than the bright blue of unvisited links. It's not so much that it's hard to see it's a link (that's too dark) but it's different enough to tell, once you're used to the site, which links are visited and which aren't at a glance.
Visited links are a luxury and may require some learning on the user side to get used to your style. They're not an absolutely critical feature of the site, whereas making links look like links is absolutely critical. This isn't to say visited links are unimportant, even if it seems they're less common these days, but unless you're using totally unstyled links (thus browser-default styled), users are going to have to learn your convention. Make it logical and confusing and you should be golden. Dark/light doesn't really matter if you're consistent and focus on demphasizing visited links.
Of course, since different sites use different conventions, it's possible you're just used to sites that make their visited links lighter. Or that the visited link color is similar to other sites' visited link color. There's lots of reasons one might not immediately grasp any one site's visited color convention, but I really don't think there's any evidence that visited links should be lighter always on all sites. Or always darker, for that matter; depending on your site's specific style, lighter or darker (or a different color altogether) may prove the better choice for making the visited link lose a bit of emphasis.
See also my answer on How to determine whether links have enough contrast? which has some relevant information on which link colors/visited links.
Visited Links should be deemphasized, I also agree with the OP, to me, it seems wrong, too, to make the visited links darker...
The short answer is that this site uses the same CSS-styling for the question lists (where it emphasises due to the surrounding white-space) as for the question content (where it de-emphasises due to the surrounding dark text). The shades are applied site-wide to the 'anchor' tags (i.e. links) instead of adjustment for context.
