I've done some research on the inside-vs-autonomous question with a focus on indymedia involvement. As some of you probably remember, indymedia decided to stay outside the official esf in florence and participated in the hub-project instead - after extensive debates and with many arguments exchanged.
The hub project turned out as a mix between reporting center and convergence center:
"a laboratory of communication, media experiments and horizontal social organisation, and the space for interactive workshops on non-hierarchical structures. A variety of media projects reflecting upon media, processes of political production, communication between activists and new forms of expression"
hub foto gallery

For ESF 2004, the options are still open. However, the 2002 debates might be of some use for those groups who are still discussing their strategies.
Here are some of the autonomy debates preceeding the ESF 2002 in Florence:

call for the hub project esf florence
concept of the hub project - outside esf, but connected
notes from "Reclaim your Media" workshop at hub project
hub/pga evaluation of need for own spaces, hubfocus on activism
imc uk report on hub project florence esf
imc uk radio london report about esf florence and hub
report about esf florence and hub
Linden Farrer - World Forum Movement: Abandon or Contaminate, argues for contamination
World Forum Movement: Abandon or Contaminate
the activity of absence - evaluation of inside/outside esf florence