There is some minor difference between the way the voice circuits are configured on the 6/6R vs. the 1000. I have both a 6R and a 1000, and the only difference I notice is that the 6R goes out of calibration quicker.
They both use the CEM 3396, although in different packages.
The 1000 has 200 RAM patch slots and 800 ROM slots. The 6/6R, as noted previously, has 100 RAM slots and no ROM slots. The factory patches are available on the Web if you look around.
It is true that the 1000 cannot be edited from the panel (except for a few system parameters). The 6/6R can, but it's so much trouble that I just the same software editor for both. Patch dumps are interchageable between the two, with one very annoying exception: The 1000 neither displays nor stores patch names. If you take a patch dump from a 6/6R, load it into a 1000, and then dump it back, all of the patch names will have been changed to default names.
The 1000 has a somewhat better MIDI implementation. It can deal with most parameter changes in real time; the 6/6R can't. The 1000 has the "guitar controller" mode, in which each of the six voices is assigned to its own MIDI channel. The 6/6R doesn't respond to MIDI Volume controller messages by default; people who do patches for them usually assign controller 7 (volume) to one of the lever inputs, and then route it to the VCA2 in the matrix to make the patch respond to volume messages. With the 1000, you don't have to do that. On the other hand, the 6/6R can do keyboard splits, which the 1000 can't.
The 6/6R has jacks for plugging in sustain and expression pedals. The 1000 doesn't, although it does respond to the MIDI messages. The 6/6R has stereo outputs, but you have to set up a split to output in stereo. The 1000 is mono out.
Somewhat to my surprise, the vacuum-fluorescent display on the 6/6R doesn't seem to have any reliability issues. Oberheim must be one of the few companies who ever figured out how to assemble and package those things properly. Both the 6/6R and the 1000 are regarded as reliable synths. Some 1000s have a power supply that hums slightly (accoustically, not electrically) and can be heard in a quiet room.
No one has ever identified that there is any difference between the black-face and white-face 1000s, other than the panel color.
Either type is a great way to get the Oberheim sound at a low price.
Switches, knobs, buttons, LEDs, LCD screens, monitors, keys, mice, jacks, sockets. Now two joysticks!