Someone else might know for sure, but I believe their 250 4-strokes (motocrossers) are exactly the same.
The "alliance" was done a couple years ago basically so they could get a better deal from component vendors (electronics, plastics, wheel parts, bearings, etc.). The KX250F and RM-Z250 were the only models that were jointly developed IIRC. To help differentiate them, I think they also used different shape radiator shrouds.
Other bikes that were basically identical included some smaller ones (KX65/RM65, plus a few others) and at least one ATV (LT-Z400/KFX400), but all those other models were pre-existing in the line-up of one company and adopted (with different colored bodywork, of course) by the other company.
As for the racing programs, both companies maintained complete separation.
But I believe that both companies feel the benefits of the alliance have run their course and are going to dissolve it in the near future if they haven't already done so.
(Edited for clarification.)
ETA: Suzuki has done this sort of thing before, though not to this degree. It has sold engines to the old (now defunct, I believe) personal watercraft company Wet Bike, as well as Bimota. Also, Arctic Cat uses the LT-Z400 as the basis for its 400cc sport ATV, which is available in two or three colors.
The 250F's are almost exactly the same except for plastic(2005 and before). Kawasaki developed the frame portion of the bike and Suzi-Q developed the motor.
For 2006, Kawasaki is throwing an aluminum frame on their 250F and leaving Suzuki with the steel frame. I think this might be the last year Suzuki and Kawasaki are going to share the 250F's because of this. From what I've read, Suzuki will be designing their own aluminum frame for their 250 for 2007 at which point they will most likely sever ties on the motocross bikes.
I don't know what they'll do with their shared models in the off-road and ATV segments, but I have a good feeling that the Yellow and Green 250 thumpers will be completely independent of each other by the 2007 model year.