Are you changing the layout and adding or moving plumbing, gas or electrical. That can get expensive. The average Kitchen remodel is 10-15 percent of the value of the house. How much counter and the grade of granite can also increase the cost. Gardenweb kitchens has a wealth of knowledge that can help you.
And here is our probable winner... Labor trumps every other cost, and the more specialized the labor, the more that it costs. The markup on labor is also normally higher than the markup on goods; if your kitchen design shop is sub-contracting the installation labor you are probably taking a bath on that, because it is probably being done on two levels if the installers are not on salary there.
Custom cabinets will be more pricey than semi-custom or stock, because of the cabinetmaker labor. Also, if some of your cabinets are the sort that are made to look like freestanding pieces of furniture, then you have explained a huge part of the cost right there -- they need finished hardwood panels on all sides rather than just frames at the back and conjoined sides. Are you going tall with the cabinets? If you go tall you can usually buy fewer of them, and the height of the doors does not add very much to the cost; width tends to add a whole lot more because trees are tall but round; the wider the panel the more it costs because each tree has fewer suitable wider pieces that can be cut from it, so wider doors usually have to be joined.
You have also added a skilled flooring professional to the mix -- wood refinishing is a much rarer skill than laying new tile, requires expensive machinery, and normally requires a team of at least two guys working for three days. (One day to sand/replace boards, one-two days to clean up dust and apply the base finish, and one to apply the final finish.)
You can very often buy your appliances and major fixtures online or at your local supply house for much less than a showroom will cost you; just have them delivered and stored at your home before the demo work begins, so that the contractor has them there when they need them. (Our appliances and fixtures were stored in our garage while the work was done -- we just had to park outside for a week or two.) If the local distributor won't sell to you directly then negotiate the markup with your contractor to purchase and pick them up for you.
Cabinet hardware has a nasty markup, so buy it yourself. Watch for clearances on the stuff -- I got ours at 60% off from a local hardware store that was being closed down; I bought them two years before we were ready to have the kitchen done, so I bought a few extras just in case. I still came out WAY ahead. Also, you don't always need the kind that are shown in the design; for instance, knobs usually cost less than handles, and you can open a suspended drawer just as easily with a knob. (Do be sure that the glides on the drawers are full-extension, however; if they are not you will be going nuts trying to get all the way to the back of them.)
PS: I have a Blanco Silgranit 10" deep single sink in Anthracite color that has been in my kitchen for 12 years now and doesn't have a scratch on it. It looks just like it did the day that it was installed. There are things that I no longer like about that kitchen, but the sink isn't one of them -- I love that sink so much that if I ever move I'm probably going to immediately put one just like it in the new house.