Today, the beta version of Bioclipse (versioned 2.0.0B20090123) was released. This release features, among others, the new JChemPaint, a new SDFEditor capable of parsing large files (tested >1Gb), a rewritten welcome page, a new console for command line access, a new Javascript editor to run scripts, etc. It also features (via online updates) optional installation of the XMPP plugin for accessing web services based on XMPP, etc.
Existing users cannot upgrade to Bioclipse 2.0beta via online updates; the version requires a fresh download from Sourceforge and read the installation guide.
More information: See the Bioclipse website and the Bioclipse development wiki.