The powerful DTrace tracing facility has some PHP-specific probes that can be enabled with --enable-dtrace. DTrace for Linux is being created by Oracle and is currently in tech preview. Currently it doesn't support userspace tracing so, in the meantime, Systemtap can be used to monitor the probes implemented in PHP. This was recently outlined in David Soria Parra's post Probing PHP with Systemtap on Linux.
His examples are using the Oracle flavor of linux, but they should work for just about any unix-based system out there. He installs the tool via a yum package and compiles the latest PHP source with the "enable-dtrace" flag. He includes a simple script to connect to an Oracle database and shows the contents of the resulting "functrace.stp". He also shows how he added more "prodbes" (the points DTrace uses to profile) into the OCI8 extension for PHP (steps and source included).