You might also take a look into global apache's error log. There are very rare cases when PHP (or, probably, other modules) causes segmentation faults in apache's child processes which prevents any request info to be written to access log. The last time I had problems with this issue it was caused by Oracle PHP extension (oci).

2009/12/3 John ORourke <john-perl@o-rourke.org>
That gives me a few new places to hunt down the issue, thanks.

Regards,
Paul