Look at this URL for a little more info.
http://www.php.net/manual/install.unix.php
In my opinion using --with-apxs to compile php as an Apache module is the way to go. You can then add and remove the php extensions you using the php.ini file. (ex. mysql, pgsql, ldap, etc) There is more documentation at the above URL.
Compiling php directly into Apache will make your scripts run a little faster. As far as I can tell, and I haven't really done any benchmarking, unless you are running a HUGE site the speed increase isn't worth the hassle of recompiling Apache every time you want to add/remove a PHP feature.
Just my thoughts.