Just spotted this thread. so it may be out of date.
I've got a 95 1100GS that has been great! I've done 18000 miles in two years and it just gets better. The only problem I've had was the head gaskets blowing in the first week, this was fixed FOC by BMW, apparently the early gaskets blew and the material has been updated, since that, despite my heavy handedness, the gaskets have remained tight.
The early gearboxes rattle at tickover, but according to Getrag the manufacturer, (quote)are the better shifting gearboxes with no pattern of mechanical defects (see
http://www.micapeak.com/bmw-gs/trans.html).
The frames were modified in an attempt to rectify the breaking frame problem when the bikes were being used heavily "Off Road". I was on the BMW off road course on the 12th & 13th of July, one of the instructers broke the gearbox on his 1150 going down a relatively gentle dip, so this problem has never really been cured. Touratech make "Hardparts" to take the strain off the gearbox on the 850/1100's.
The biggest pain with the early 1100's is the bare alloy wheel rims, as opposed to the anodised later ones, A serious investment in autosol is required to keep them clean.
I'm sure theres many more differences between the model years but there all damm good bikes.
Rob Farmer
95 R1100GS
Loughborough
Leicestershire