When organizing a kitchen in a new apartment, I usually start with the stove and sink (which are presumably fixed in position) and work out from there.
I like to have my cooking utensils (spatulas, stirring spoons, etc.) and spices near the stove and easily accessible (not in a drawer or cupboard). I’d second hossman’s advice to hang pots and pans above or next to the stove. Having them out will maximize your cupboard space, since they’re large and hard to stack.
At this point you should still have all of your drawers and cupboards empty. Now I turn towards the sink. You'll want to put a drying rack next to it. And you'll want to locate the cupboards and draws for your most-washed items (for me, mugs, cups, and silverware) near the drying rack so that they're easy to put away (this should be no problem, since it’s a small kitchen). I try to balance this with putting silverware in an end drawer (as opposed to one in the middle of a row of drawers), closest to the regular dining area. Less frequently used dishes should go higher up, almost out of reach (for me, stemware).
I also support kevbo’s sentiment of not necessarily putting dishes together just because they are of the same type. It’s probably optimal to stack all of your plates in the same cupboard, but this is simply not true for mugs. Most people have more mugs than they know what to do with, since they’re common give-aways. Worst of all, they don’t stack! Take your six favorite mugs and put them in an easily accessible location (if you’re paying attention, that’s an arm-level shelf in a cupboard, close to the sink). Then take the rest and put them in a less-accessible spot, not necessarily in the kitchen. There’s no reason to fill all of your best space with mugs.
Put your trash can under the sink so it won’t make the kitchen stink, but don’t be afraid to pull it out when you’re cooking.
Use the top of your refrigerator for storage, but not for things sensitive to heat or breakable (especially if you live on a fault line). For the top of the fridge, I want to say one word to you. Just one word. Are you listening? Plastics.