Start with what you have: You may love them, you may hate them, but unless you've got the money for a full scale renovation, your sink, stove and refrigerator aren't going anywhere. Their position will dictate where everything else goes. Cleaning them up (Magic sponges, Barkeeper's Friend, Mrs. Meyer's All Purpose Spray, Bon Ami and those curly stainless steel sponges sometimes called Kurly Kate's, are my weapons of choice), inside and out, can go a long way towards making them presentable.
Create stations: Taking a cue from restaurant kitchens, mentally assign stations for all of the tasks that you do in your kitchen: cleaning, storage, prepping, cooking, putting food away. I bake a lot, so I also have a baking station.
Organize items according to task: The point is to organize the kitchen so that there's as little unnecessary movement as possible. If, after you've washed the cutlery from tonight's dinner at the sink, putting it away means walking across the kitchen to do so, chances are it will never get put away, no matter how pretty the cutlery drawer organizer is.
Move things around so that what you need is in arm's reach: Cutlery and dishes should be near the sink; spices and cooking implements, whether rubber spatula or skillet, should be near the stove; put knives and chopping boards near your prep area; store sugar, flour, rolling pins, cookie sheets and standing mixer near your baking area.
Out of reach: Put things you rarely use — the turkey platter you pull out at Thanksgiving, the holiday-themed cookie cutters — higher up or lower down. Having to get on a ladder, or even bend your knees, means you'll use something less frequently.
If necessary, buy two: I use cinnamon for cooking and for baking, so I've got one canister near the stove and one in my baking area. While I'm not suggesting you buy two food prep machines, consider doubling up on little items like spices and spatulas.
Merchandise your storage: Yes, I confess, my kitchen is always ready for its close up. I like my kitchen organized, I also like it pretty. Arranging items by size and color as well as by how often you use them can go a long way towards making your time in this room pleasant.
Pretty but also useful: If the canister that you use to store flour is hard to open, it's not useful. Before you buy something, try it out in the store and consider how you'll use it. Does it feel substantial in your hand but also light enough that it's easy to use? Can you open a container with one hand? I've removed rubber sealant rings from many a flour container in order to make them easier to open.
Stick with the place you've given for things: With everything in my kitchen assigned a spot, it's easy to see what I have and what's missing. With a quick glance into my refrigerator, I can tell that I'm out of butter or milk or low on veggies. Since I always keep these things in the same place, a glance at my kitchen cupboards tells me I'm out of glasses and I'd better get washing!
(Images: 1. John's New York City Interior with a California Garden, 2. Abigail Stone)