I feel like I subconsciously ignore the "Linked" section to the right of questions.
Is it just me, or would it be a good idea if it stood out more prominently?
Of course you ignore it. It's in the right-hand sidebar. That's where ads live.
IMHO, that's just fine, most of the time - after all, if you're focusing on the main content area you'll probably see the very same links since that's where they come from...
I look over at the "Linked" and "Related" sections when I'm trying to track down a post and my search brings up something similar but not quite what I want - often enough, those two sidebar tools will lead me to it. But I wouldn't want them intruding on my view once I have found the page I want to read. That's the sort of dirty trick ads like to pull.