NetBeans for PHP uses xdebug, in which you can set breakpoints among other functionality. It's the best IDE for PHP I've tried (and I've tried alot of IDEs).
From http://www.netbeans.org/features/php/index.html
Debug PHP code using Xdebug: You can
inspect local variables, set watches,
set breakpoints, and evaluate code
live. Navigate to declarations, types
and files using Go To shortcuts and
hypertext links. Use a global PHP
include path for all projects or
customize it per project.
The NetBeans IDE for PHP also offers
command-line debugging: The PHP
program output appears in a command
line display in the IDE itself and you
can inspect the generated HTML without
having to switch to a browser.
You can debug scripts and web pages,
either locally or remotely. The
NetBeans PHP debugger integration
allows you to map server paths to
local paths to enable remote
debugging.
I've looked up Eclipse PDT as well, and it uses Zend Debugger (or xdebug, but ZD seems to be the default debugger). I have never used it (I have used Aptana Studio, a Eclipse sub project, didn't like it) but Eclipse is a solid IDE and used widely. I have never had the need for trading away NetBeans for Eclipse thou. Anyway - IBM wrote a white paper on debugging PHP in Eclipse PDT using Zend Debugger. Happy reading. ;)