I am involved in an exciting new initiative that works to overcome collaboration problems. This new initiative (that emerged from ParticipationCamp) is called OpenKollab and we set out to providing a space where projects can get support for answering these questions. OpenKollab is both a community and a platform, with a mix of technologist and process oriented people driving it. Check out the wiki and tune into the IRC channel #openkollab and get involved if you believe in openness and want to experiment with new forms of collaboration.
Questions we should ask: How do our projects share data? How do our projects share users? How do our projects share impact? How do our projects connect with other projects? Should we be collaborating on another project rather than inventing another wheel?