This probably doesn't address all of your concerns, but if you use kernel-package to generate a kernel-image*.deb package, it will include the .config file as /boot/config-KERNELVERSION. That will at least let you see what options were selected for an installed kernel, and can be copied to your source tree as the basis for a new compile.
You can keep the names of the kernel-image packages unique by manipulating the "debian version" portion of the name (I tend to use descriptive versions, like "smp.1", etc.), and so can generate as many as you like on the box of your choice. Then you just need to distribute the deb-files to the appropriate systems for installation. > I now have several networked Linux boxes; but they all have different > hardware and do different things and they have different kernels. > > I have trouble keeping track of what options are compiled into which > kernels and I'm beginning to be frustrated. Can anyone suggest a way > of doing this? > > Ideally, I'd like to keep a file with the options in it somewhere, be > able to change one option and recompile the kernel. I'd also like to > be able to do it on one central system that's faster than the others.