As part of the work I've been doing to answer this question about the technical workings of a glitch in Pokémon Red, I've been looking for a way to use a standard debugger to debug a Game Boy ROM. Although many of the emulators I've found have some support for debugging, nothing I've found so far has been helpful.
As a background, as of now I have tried to use the Visual Boy Advance built-in features to do debugging, but they aren't particularly useful for what I'm trying to do. VBA lacks the ability to set breakpoints, and since it steps forward at the level of frames rather than instructions I'm unable to see how the code is executing when I actually need it to. Although VBA says that it supports GDB debugging, I have been completely unable to get it working. I tried cross-compiling GDB for ARM as per the instructions, but could not get GDB to connect to the emulator (it would recognize that there was a program to connect to, but reported that the protocol had been violated). I repeated this with similar success in both Windows with Cygwin and on Ubuntu Linux. A friend and I tried to use Insight/GDB, but ran into exactly the same problems.
I also tried to use the NO$GBA debugger, but it refused to load my ROM for Pokémon Red (and then insulted me by saying that nothing I could try to do would fix it, as the file was just flat-out wrong).
Additionally, I tried downloading this version of Visual Boy Advance that claims to have a debugger in it, but for some reason I can't get it to enable the debugger. Pressing F11 as per its instructions has no effect whatsoever.
I believe that I've done my due diligence trying to get a debugger working, and I'm surprised that not a single one of them has worked. Does anyone know of a simple, straightforward way to debug Game Boy games using standard debugging techniques? I'm interested mostly in being able to put in memory write breakpoints (to see what routine is clobbering certain parts of memory). I would really appreciate it if someone with first-hand experience doing this could provide details on how to do this, as online resources on the subject seem pretty limited.