A few things seemed to have changed with Trac once I dist-upgraded Trac on Lenny.
ScriptAlias /~sburke/skynet06 /usr/share/trac/cgi-bin/trac.cgi
/usr/share/trac/cgi-bin/trac.cgi didn't exit.
Find new Trac files
dpkg -L trac | grep cgi
This gave, amongst other results: /usr/share/pyshared/trac/web/cgi_frontend.py
Replacement line of code:
ScriptAlias /~sburke/skynet06 /usr/share/pyshared/trac/web/cgi_frontend.py
chmod 755 /usr/share/pyshared/trac/web/cgi_frontend.py
Another error 500 from Apache.
su - sburke trac-admin /home/sburke/sustainabilityportal upgrade