As far as I am aware, there is no real difference in sound quality.

The 4000s in my opinion are far superior sonically, especially the Mk1s. You do lose the display though. 4000s are in my opinion the unsung heroes of the Beolab range - compact but quite powerful enough and plenty of bass. They are now available at a good price too.

I have both BL4000 mk1s and a BL3500 mk2.  The BL4000s are sonically much better than the BL3500. 

However, do you need this superior performance in your office?  I'm perfectly happy with the BL3500 in my kitchen.  I used to have the BL4000s in the kitchen, and they were overkill.  Also, I've heard rumors on this site that the BL4000 mk2's are not as good as the mk1's.

Stan

FWIIW, I have a pair of BL4000 MkIs in my home office ML system, but I found them too bass-deficient for my tastes, shortly thereafter added a spare BL2 subwoofer that I had on hand, and found the overall sound balance far better with the latter. The 4000s are simply sitting on a long desk, one at either end, using the inexpensive plastic B&O stands that raise them a few inches off the desktop surface. They would probably sound even better if I mounted them on the wall behind the desk, but I have been too lazy to get around to the task. Temporary solutions have a way of becoming permanent...

I agree with the others even though I have BL4s - I bought them for portability rather than superior sound quality

This weekend I am going to try the suggestion of BL3 rubber rings to raise the BL4s and see if that improves their performance

Nett nett ... pick the 4000s

Well, thank you all for your contributions! I finally made a decision in my short list of possible speakers, being BL4000 (plus IR eye), BL4 ( plus the same) and BL3500. Last week I visited my dealer and I must say from an acoustical point of view and listening experience the BL4000's MK1 are (by far) the best choice. However I agree with Stan, if you do not need the better BL4000 performance in a rather small (11 m2) link room, the BL3500 is a very balanced choice. So I bought a very mint 2009 BL3500 for an even interesting price and it just performs what I expect it to do in my PC room. Very happy with this solution. A well finished B&O project again!

Once again, thank you all for your answers.