Ok Dishwasher, dedicated ice maker WILL be problems, so some areas will
HAVE to use 36 inch counters.

Not a "problem", necessarily - if you are going to be doing custom
cabinetry and you REALLY don't care about resale value, there is no
reason not to consider placing every work surface at a height optimized
for functionality

For example kitchen designers sometimes specify a dishwasher placed
8"-12" off the floor, this makes it easier to reach the bottom rack:

http://www.tndhomes.com/tndandud_images/wellborn_dw.jpg

and many lines of semi-custom cabinets provide this feature as an
option, for example, here's KraftMaid's:

http://images.kraftmaid.com/whykm/me...Dishwasher.jpg

Such layouts sometimes also specify a lowered counter height for
cook-tops (makes it easier to see what's in pots) and/or for food prep
areas.

Once you are free of design "standards" you can get pretty creative;
one custom installation I've seen placed a marble counter top for
rolling out pastry dough around 30" off the floor and cooled it by
placement over a "mini" refrigerator with it's top cut open and set
into a low cabinet supporting the counter top - when not in use the
rolling surface was insualted by a cutting board with rigid foam on the
bottom.

Michael Thomas
Paragon Home Inspection LLC
Chicago, IL
mdtATparagoninspectsDOTcom