Blogging company Six Apart will soon announce it has purchased Rojo, the web-based feed reader, for undisclosed terms.

Six Apart won’t be adding an aggregator based on Rojo, but instead incorporating some elements of the technology into its existing products, according to Six Apart CEO Barak Berkowitz. Rojo CEO Chris Alden will run Six Apart’s Movable Type group.

Alden, a co-founder of Red Herring, is being tapped for his media experience, says Berkowitz. Aaron Emigh, chief technology office of Rojo is also joining Six Apart, so are many other employees. Some of Rojo employees have found home at other start-ups, such as BitTorrent.

In a chat earlier today, the two talked about spinning out the Rojo.com (the online feed reader) and Rojo’s weekly feed roundup newsletter into a separate company, that will look for outside investors. Or atleast that seems to be the plan for now. “The service is going to stay up, and we are going to use the code in some our other products,” says Berkowitz, who seemed pretty pleased with his latest acquisition.

Things could have been a lot worse for Rojo, but it seems that the Valley network has saved the company from airing its problems in public. Rojo, founded in 2003, was perhaps a bit ahead of its time, building in tag-based browsing, user voting, and community recommendations early on. The site never managed to build much of a user base — according to a May WSJ article, Rojo had just 100,000 unique visitors per month. We tried using it ourselves but it never stuck.

Rojo had raised over $3.5 million in funding from TPG Ventures, BV Capital, Marc Andreessen, and Ron Conway, among others, though it hadn’t added new money since 2004. Meanwhile, Six Apart recently raised $12 million just because it could. The company is capitalizing on its role as a little giant; it also recently bought out SplashData and its mobile blogging product.

There are getting to be fewer and fewer RSS reader companies — Ask bought Bloglines, of course; a little company called SearchFox died (and might have been partially acquired by Yahoo); Pluck is focused on other things.

Who else is left? NewsGator was trying to make a play by buying everybody, but all we hear about from them these days is the enterprise; Attensa is pushing the marketing pedal hard, and seems to be sponsoring every industry event that they can sponsor. Personalizable home pages and memetrackers are a younger category, but Newroo was already bought by Fox Interactive. Go ahead and say it if you like: it’s only a feature.

(With reports from Om Malik)