I would definitely get the taller cabinets if the upcharge is reasonable, especially since you don't have a lot of them. I have 42" uppers with 96" ceilings. I could go to 39" but not 36".

17" is probably enough room below the wall cabinets, but check your countertop appliances to be certain.

Definitely 39", no question. 36" is short, will cut your storage space, and will make your ceilings look lower. How big are your crown moldings? I would rather shave an inch off those than have to shave the inch between the counter and uppers. What kind of undercabinet lighting will you have? If it is LEDs which are very small, you should be OK with 17", but again, I'd rather have a smaller crown. Since you said it is a cottage home, and I get the sense your decor is not elaborate, a minimal 2" crown molding would look fine. I think multi-layered crown moldings are pretty in a library/den/living room, but not necessary in a kitchen.

I think I agree with akchicago. I just installed our crown moldings. They are plain in profile and 3 inches in height, which I thought would be fairly demure. Upon installation, they appear fairly beefy to my eye.

For our 101" ceiling, we chose 36" base cabs+17.5" BS+1.5" light rail + 43" uppers + 3" crown. You have 5 fewer inches to work with, so I think cutting 4 from the box and 1 from the crown, as akchicago suggests, would work well.

Caveat: If you ceiling is not very level, it takes a larger crown to hide the variation.

We have 96" ceilings. We went with 42" uppers and have 17 1/2" from counter to upper cab (doing the backsplash today so that meausurement is fresh!!!). it's plenty of clearance. I would definitely go with 39" for the extra storage space.

I had to make the same call - We're lowering the cabinets about 1/2-1" (plus we're using a lightrail, so there will be even less than 17" space above the counter top. But smaller crown looked too overwhelmed with the 39" cabinets and my architect said that 36" cabinets with 3" crown would be out of proportion and contradict the style of the house and kitchen (we have shaker type doors). I have simple 2" crown throughout my 1939 built house. I don't keep appliances on the counter top and have a large island, so I'm not concerned about shorter space below the wall cabinets. I wish I could send you a picture, but we're ordering cabinets this week :)

Go with 39" and order an extra shelf for at least a couple of the cabinets. My wall cabinets are 36" and 42" and I have an extra shelf in all of them. It keeps you from having to stack things and even a short space at the top shelf makes it good storage for infrequently used things. Doesn't work for cereal boxes but that's about it.

Yes on taller and double yes on extra shelves (or plan to make them yourself if they are pricey). I'd try to get the 18" space, although I don't have a good reason to do so. But if there's room to hang 'em a bit higher, go for it. You'll be climbing on the counter for those top things anyway.

File cereal boxes on their sides!

It'll look good and you need the storage. And even 17" will be fine unless you really planned on sticking your 17.5" mixer under them.

factor the width of the door as well...I would not want to open anything wider than 18" at the extra tall height, and 15" max width would be better.

Thanks everyone for your comments! I went with the 39 cabs that will be attached to a 3 inch straight molding at the ceiling line. This molding has a tiny lip and the 2 in crown will go on the ceiling and hit this filler piece above the lip and this should allow for anything that is uneven. And I chose a simple bottom molding again with a small lip (I know that's not the right term but I forgot what the KD called it). Does everyone do u/c lighting?

In answer to your question, not everyone does u/c lighting, but I couldn't function in my kitchen without mine. My ceiling cans are poorly placed and create shadows, making my counter too dark to use at night without the u/c lights. I also love how I can dim them, and not have the ceiling lights on at all, and have lovely soft mood lighting. I have Juno xenons, which have a nice bright white light, and do not run hot. Love them! Also look into the LEDs which are really tiny. They are great. But if you choose LEDs, choose carefully, because some of them are not bright enough. There is a Lighting Forum on the Gardenweb that may have more info.

Thanks akchicago. I have made a note about this as this might be something I will have to look into down the road but I love the visual image you provided. I would not have thought about being able to dim them, that's for sure!