in reply to Closing stdout on CGI early.
If Apache requires your program to exit to close out the browser, one possibility would be to close STDOUT and fork() and have the child do the work and the parent can exit when its done with the output.
If you ever move to mod_perl this will defeat the reduction in startup overhead since you will need to start a new script every time anyway. If it doesn't break mod_perl entirely by exiting early.
For mornal CGI this may work ok for you.
Update: Another thought. I have a system which needs some slowly changing data from another database so I have a daemon process that listens on a FIFO and my CGI script writes an information request to the FIFO and then goes on with its life.
The daemon process then reads the FIFO and gets the updates independant from the web process completely. The FIFO is checked in non blocking mode by the CGI for obvious reasons and the update request is just skipped by the CGI if the FIFO isn't ready to read data for any reason.
As a side benefit the web system can run 'offline' for a while completely transparent to the end users.