First off the bat, I didn't see the cool colours of the bootup process telling me that I have a logitech cordless mouse, and all of the other autoconfiguration that the Knoppix CD did. Instead, I got a very plain white text on blackbackground boot process with no progress bars or anything.
Thats because you dont have a knoppix-cd, but an 'normal' debian system. so no nice, colorful hardware-detection (because it is already configured) but just plain startup. I prefer it colorful myself too, but I can live without it

Fourth, after installing Synaptic through apt-get, I could not load up my sources list. Synaptic would complain about not being able to read the file sources.list. Manually editing this file worked however.
I have the same problem. dunno why...

Fifth, performing an "apt-get update" and then "apt-get upgrade world" would tell me that about 120 packages would be removed (mostly KDE packages with K3B being one of them). Knoppix should maintain a package mirror for the packages that it has installed by default so that these packages aren't removed.
I have the very same problem ("apt-get upgrade" without "world" does the same) and I dont like it either... must be some bug, broken dependency's or what? After some trying, It looks to me it has *something* to do with libvorbis0 and/or libvorbis0a ??? But im unsure...

Sixth, the bootup and shutdown voices are gone. When I replace the voices in the KDE setup (this involved setting arts to start automatically), they aren't heard before the KDE boot box starts (like the Knoppix CD), they are heard after KDE configures the devices and such. And, the shutdown voice gets cut off as KDE exits whereas the CD allows the voice to complete.
Guess the reason is as like with 1: its not knoppix anymore, but just debian. But there might be some hacks to solve it, and I'd like to have them too - so if you find out, notice, and maybe they can be included in knoppix for the hd-install ??!!!??