I've been surfing the net since it's inception. I can say that I perceive underlined text of the fore color to be plain text, and underlined; or not underlined text of a different color as possible links, and I usually hover over them if not underlined and observe the status bar to see if this is so. I also perceive text in a box as a button to a link and hover it as well looking for a tool tip etc.
I think most people would do the same, although I have read articles where a link was provided in a different color, not underlined and it was missed by its intended audience. Like anything else, there is no perfect way, but there are good standards available as mentioned by AEJBUG.
Following good standards, like following good language conventions improves communications and isn't that what the W3 is all about?