In my mind, the kitchen revolves around the oven and stove so that is where I start when organizing a kitchen. I usually put the pots and pans to the right since I am right handed, but any lower cabinet near your oven will work. I like to put the glassware either by the fridge or by the drying area; it was more convenient in this kitchen to put them above the drying area. That cabinet was also perfect for my bowls and coffee cups. I save the tall cabinets for J's things since I can't reach that high without standing on a chair.
I don't like to waste floor space with a trash can, so we store ours under the sink along with cleaning supplies. I have my nespresso machine out for easy morning access and the pods are stored in the shallow drawer right there. The large cabinet under the drawer is on the outer edge of the kitchen but near prep space and an outlet, so that is where I store my appliances. J and I can just reach into the cabinet and put the appliance directly where we will be using it without taking any steps.
You can see in the picture above that I have stored my flatware in the drawer under the drying area. This allows for convenient "putting up" (J makes fun of that phrase every time I say it). The flatware and glassware are also right next to my casual dishes. Mom says to store your dishes near where you are plating your meal, which means right next to the stove in this tiny kitchen. I have the casual dishes on the right near the drying area since we use those most often, and the formal dishes to the left. The cabinet above the stove is perfect for keeping my empty glass jars since it is a bit high for me to easily access every day.
I am lucky to have two skinny cabinets on either side of my oven. On side is for cutting boards, near my prep space, and the other is for cookie sheets and pizza stones. I keep my cast irons inside the oven.
My main prep area is to the left of the stove. I find it convenient to have my measuring cups, trivets, food storage, and baking stuff all on that side. I keep my kitchen aid out because it is too heavy for me to lift it from a lower cabinet. When I want to bake, I just pull it forward while in use and my baking stuff is right underneath where I need to work. This side of the kitchen has more storage space, so it catches all the random pieces (hence disaster zone).
Having colanders and mixing bowls either near your fridge or prep space makes it easier to get your cooking done quickly. After the meal, the prep space turns into the cleaning up space so I also keep my food storage on that side. And of course, oven mitts near the oven makes perfect sense.
Here are some closeups of my counter space. I don't like carrying big bags of flour and sugar out of the pantry whenever I want to cook or bake, so I have three canisters (thanks, Melinda!) to keep those two items and rice near my prep space and stove. The knife block stays out, as does the bread basket and produce bowl. I haven't found a home for my dutch oven, mostly because it is so pretty I love to look at it. I will probably put it into the oven if I ever need more prep space, but so far it's placement hasn't gotten in my way.
I keep everything I need for stovetop cooking to the right of the oven (this is a good thing for right handed people). I keep my vinegars, cooking red wine, and olive oil in old wine bottles with pourers. These bottles are better sized for my hands than the containers these things come in. I have canisters for my wooden spoons and other cooking utensils. I also use my jelly container for garlic. It bothers J that the word doesn't match the contents, but I don't mind it. If I need more space, I can put up the second drying mat but usually I don't need to do that.
I do have a small pantry (not pictured) on the other side of the fridge, which allows all my cabinets to be used for kitchen stuff. The space may be small but I have found a way to make it work for my kitchen habits and belongings. I shifted things around slightly after the preliminary unpacking and organizing as I discovered my most common uses of the counters, and you should too. It really doesn't take that much time to totally swap two giant cabinets full of pots/pans/baking stuff. Trust me, I have done it. If you have an kitchen organization tips, share with us!