I typically use the Geiger build, but just as a debugger. I use
XVI32 or
HxD as my hex editors, but if I'm on the go, I'll use a basic hex editor for Android.
Not to any degree near what I've read on some of the forums, I tend to make builds. So, I may do some hex editing, or perhaps some tile changes via
TileMolester, or change some palettes via
SNESPal, but I'll use
Lunar IPS to make patches. Then, I'll make a .bat file and have it run either
xkas (for ASM) or
flips (for .ips patches) against a copy of the original ROM. That way, where one patch in the build fails or can be improved, I can just strip it out without really impacting the rest of my changes.
Admittedly, I've gone a little crazy with the patches and ASM files for my last (and next) hack, but it has been helpful in keeping track of what I'm doing.