A couple of weeks ago I moved my Instapaper account over to Pocket. The reason for the move was that I wanted better organisation of the articles that I had read and that meant more than just being able to file what I had read into folders. Don't get me wrong, Instapaper is great for taking content and making it easy to read, but after that you can only file what you have read into folders. Instapaper does offer a full-text search facility in their premium plan but I found that I needed something in between folders and searching.
Pocket caught my eye when it first came out as a re-brand of Read It Later. I did trial it for a few days but it duplicated what I already had in both Instapaper and Pinboard. Since then I've moved on from Pinboard and I handle my bookmarking needs with a collection of Markdown files. What I needed was better organisation of what I had read. Searching amongst hundreds of articles is okay for unique keywords but I have a lot of articles on web development and some of them are difficult to find.
Pocket offers more than just the ability to queue up articles to read. Tags allow you to organise what you have read and there's full-text search also. Lastly Pocket stores a copy of the article for you should the original go missing. Those last two features are in Pocket's premium plan, but at just $45 for the whole year, I would say that it is worth it.
The only problem I have is that when I imported my Instapaper articles into Pocket, I had over 3,500 articles. That's a lot of articles to tag and I will eventually get round to tagging everything that I keep. It's not all bad though. During the import Pocket tags articles with their original folder name in Instapaper, so I have some form of organisation to start with. Also, it gives me a chance to check my archive and remove articles that are irrelevant. Lastly, Pocket offer clients for OSX, iOS and Android and there is also the web client which anyone can use regardless of your preferred platform.
Instapaper is a great service for those that want to read and archive their content and I would still recommend them. If though you want a little more organisation to what you've read, then I think Pocket might be a better fit.