I finally got fed up with there not being a good utility for making FAT-images for OS development, so I made (though not finished yet) my own file system and utility to add/remove files to an image with this FS. This file system is currently (rather conservatively) named Matte File System. It is in a very early stage, but it supports folders, files and pretty much all the basic IO stuff.
By using my own file system instead of FAT or ISO or something else, I will know exactly how the file system works. It also gives me greater control of the sectors, especially the boot sector. I will probably be writing my OS from scratch using this file system, though not the current version, which is pretty limited - though the system supports it, files can currently not be larger than 512 bytes.
So, I just loaded my kernel (which just prints a message in green at the moment) with my boot loader in my own file system, which I guess is pretty cool.
The utility for making images with the file system in question (which also compiles the kernel and boot sector at the moment):