There will be big changes - it will be more a rewrite than update of WinMerge 2.x. Major things to happen:
- It will be a cross-platform software. Most likely GUI will be created based on Qt. At least nobody has had any realistic ideas to use other frameworks.
- Development will happen in Mercurial repository hosted at Bitbucket. Mercurial allows distributed development and that makes our workflows much easier and faster when applying changes from different people. Also Bitbucket is much better Mercurial service than Sf.net where Mercurial is one of those second-class service citizens.
- Most components we use will change.
- Translation system will change. Though we might still use PO files as public API for translators. We'll see...
- Licensing might change. If we get permissions from relevant people we'd like to use LGPL 2 license in future.
- Feature list will change dramatically - we'll take a critical look at what can be done and maintained in future.
It is worth emphasizing that this will be a lots of work. For few developers. So don't expect us to have a "stable" release anytime soon. It will take time. Realistically speaking first alpha-level release having minimal set of features working might happen after the summer.
If you want it to happen faster then you need to get involved and start helping us to get it done.

We already separated Web pages to separate Mercurial repository at http://bitbucket.org/kimmov/winmerge-web. Web folder in Sf.net SVN won't be updated anymore.
If you want to help - first thing is to start participating discussions in this forum. If there is no existing topic yet - create new topic. There is no WinMerge 3 code yet. But you can use my winmergeqttest and libxdiff-testing -repositories. Especially ideas how to create current WinMerge editor features (diff block coloring is the most important) with QScintilla would be welcome.