Hi Marco,
There seems to be some kind of linkage problem since we never actually succeded in linking eclipse with basex ("Error: Could not find or load main class") even when following the tut at: http://docs.basex.org/wiki/Integrating_Eclipse
What’s the complete error message? Do you have some more information on the Eclipse and BaseX version you have tried? It should work fine with any recent version of BaseX, Eclipse Indigo and the XQDT update link, and most other configurations we have tried so far.