Today, Bioclipse 2.0.0A20081028 was released. For existing users: Bioclipse should pick this up and ask for upgrade automatically, but you can always choose menu "Search for extensions..." to manually start the upgrade.
The upgrade brings numerous bug fixes to Bioclipse, but the new JChemPaint and CDK1.2 rendering are not included yet. Bioclipse 2.0.0 is preliminary scheduled for release in mid December, and will contain a new 2D-editor for chemical structures (JChemPaint 3), a new MoleculesTable (for editing large lists of molecules like SDFiles, database queries etc), a new Jmol feature with stable Jmol interaction, search/retrieval/editing/upload of various spectra, and a plugin for local chemical databases (StructureDB). More features (QSAR, Pharmacophores etc) will be available in early 2009.
Get Bioclipse 2.0.0 alpha02 at Sourceforge and read the installation guide.
The Bioclipse Team