I have talked a lot about about integrating Jalview into Bioclipse for visualization and editing of multiple sequence alignments. I spent some hours on the problem and it was not too hard to get things going. It's now possible to double-click an alignment in any of the formats supported by Jalview (fasta, msf, clustalw, pileup, pir, blc, pfam) and Bioclipse opens an Alignment Editor with Jalview on one tab and the source file on the second.
It is currently not possible to interact with Jalview via the mouse, this needs some wrapping of functionality into SWT actions and menus. But it's a good start :-). See the wiki page net.bioclipse.jalview for progress.