Since I am ADD and OCD, I upgraded to the 2.6.31.6 kernel last night and though I have not checked all my apps, everything seems to be in order. I thought I would share the steps I used. Keep in mind that this was done on BT4 (pre) final which is installed on my HDD. The following steps are also unique to the 2.6.31.6 kernel and should be adjusted accordingly for the specific kernel you are building.

The first thing I did was to make sure my distro was current using apt-get.

You can retrieve the latest kernel from kernel.org. Once it is downloaded you need to move/copy it to /usr/src. Then, as root from a shell:

1) cd /usr/src
2) tar xvjf linux-2.6.31.6.tar.bz2
3) cd linux-2.6.31.6
4) zcat /proc/config.gz > .config
5) make menuconfig
(You are on your own with this step in that the kernel for each computer is architecture specific. If you are at a loss here then either learn what to do in this step or don't compile a new kernel. Mistakes in this step may possibly be disastrous. Consider yourself warned.)
6) make
(This may take a fair amount of time.)
7) make modules
8) make modules_install
9) mkinitramfs -o /boot/initrd.img-2.6.31.6 2.6.31.6
10) cp /usr/src/linux-2.6.31.6/arch/x86/boot/bzImage /boot/vmlinuz-2.6.30.5
11) cp /usr/src/linux-2.6.31.6/System.map /boot/System.map-2.6.31.6
12) Edit /boot/grub/menu.lst to boot into the new kernel.
(I merely copied the existing boot entry, pasted it above the old one and modified it to show the new vmlinuz and initrd.img. This left the old boot image in place in case something went terribly wrong with the new kernel.)
13) reboot
14) (from a shell) sudo fix-splash

You should now have a shiny new kernel.

Disclaimer: As I said, I have not yet had the time to run this kernel through the paces. It is NOT customized for BT4 nor Debian and I may very well have broken some of my apps by upgrading. As I also said, I was too ADD/OCD to resist. I trust some of the vets will tell us if and why this upgrade may or may not be a bad idea.

Props to admrt for his post which provided the info I needed to get this done.