PCSX2 Breakpoint Tool allows for breakpoint debugging with current PCSX2 builds (older versions included this capability).
How to use it
The 'Set Executable Breakpoints' control group is a way to keep track of current program breakpoints as well as generate PNACH lines which include the 'break' instruction.
Enter the address(es) to break at into the 'Breakpoints' text box and click 'Generate' to create PNACH lines which insert breakpoints at those addresses (these must be copied to a PNACH in the PCSX2 'cheats' directory named with the game's CRC).
After entering breakpoints run the game in PCSX2 until the game freezes - this means that the 'break' instruction has executed.
Create a save state while the game is frozen then open that save state by clicking 'Browse' or dragging and dropping the p2s file.
The 'View State' control group is used to view the state of Emotion engine registers (PC, $0-$31 and $f0-$f31) when the save state was made.