Is there an application or a site grouping addresses by user graphically? Addresses can be grouped as belonging to the same user (or, better, same "account") by grouping together the addresses that participate as inputs to a single transaction, and doing it transitively. This has been done in the recent paper by Shamir and Ron, by some previous researchers and can be done by znort's parser. I know this is not 100 % accurate but I'm fine with it.

What I'm looking for is a site that displays the results of such grouping graphically, possibly with transactions between accounts as well.

I've read about such a site on bitcointalk.org, but I can't find the topic any more. I'm looking for the url of the (now possibly defunct) site or the bitcointalk topic describing it.
The tool is called Blockviewer.  The website, blockviewer.com, no longer exists.  However, the source code is available on Github: https://github.com/thallium205/BitcoinVisualizer.  Thus, you might be able to download the source code, compile it, and run it on your own machine.

You can also read the original blog post introducing some of the ideas behind it.