I’m generally not pleased when a user interface does something I didn’t intend it to do. Such as when I click on a link but instead of taking me to a new page, it pops up an overlay with advertising or related content (see this Yahoo News article or any website “enhanced” with Vibrant Media to see what I mean).

So I really should resist the idea behind Apture, a startup founded by three Stanford computer science students that aims to improve contextual popups rather than ban them. But its technology and user interface is actually quite good, even if it does require users to change their expectations a bit.

Publishers can use Apture to enhance their writing by adding links to popups (or HTML-based “overlays”) that display relevant media from sources such as Wikipedia, IMDB, Scribd, Google Maps, Hulu, ESPN, YouTube, Imeem, and Flickr.

Installing Apture is easy: just drop a snippet of JavaScript code onto your site and begin manually choosing the sections of your writing that you want to turn into popup triggers. Related media content can also be added between paragraphs as embeds. The publisher interface, like the end-user experience, overlays the page’s content, making setup a matter of point-and-clicking.

Let’s say I’m talking about Redmond, Washington or Family Guy or David Bowie. See those links? If you click on them, popups will appear that shed light on what they reference. And the popups will lead you off to other, related popups that can be used to learn even more.

Apture’s publisher tool has been available to 2,500 blogs (including a couple blogs run by the Washington Post) since April. Over the past couple months, the company has worked on improving the user interface and adding support for additional sources. The tool is now being made available to everyone.

As a publisher, there are a few concerns that come to mind when considering a tool like Apture. As mentioned before, it requires users to change their expectations. It also requires publishers to change their own habits (especially if they have to add these links after their content is live). And it might even cut down on page views when used to showcase internal media in lieu of hard links. Perhaps a way to get around two of these issues would be to make the link’s icon trigger an overlay but leave the link itself as a normal one.

Apture is based in San Mateo, California and has raised an undisclosed amount of angel funding since its founding in February 2007.