There are a few reasons why you would want to build your own kernel:

1) Optimize it specifically for your CPU.
2) Trim it down to only fit your hardware (less modules cq hardware
support)
3) You have written some modules of your own.
4) You want to live on the bleeding edge or help testing new
features...

I have always build my own kernel for reasons 1 and 2. On my server I
don't need usb, audio, serial & parallel port, floppydrive, (FAT(32)
filesystem) support, so I didn't build the modules for those parts,
this saves some kernel memory, the hardware is still there but
unused...
My kernel is specifically optimized for a Pentium III Coppermine) and
therefore only runs on a Pentium III and above. (Makes the kernel
possibly a bit smaller and faster just for my CPU type.

I don't know the changes the Debian team has made to the plain vanilla
kernel, but you have to be sure you pick the right options during
configuration, otherwise it possibly won't work at all...
Maybe you should start with a 'make allmodconfig' and after that change
some items in 'make menuconfig' you're really sure about. That should be
the safest way to build your own kernel...
For the rest: see the post of bhaagensen


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