Storage and Organization

Its one thing to own all the right equipment and have stock of basic ingredients. Its another beast to make sure that all your food is stored properly and that your equipment is easily accessible.
Microorganisms, such as bacteria and viruses, will thrive in your food at temperatures ranging from 40F to 140F. Insects and parasites will slither their way through nooks and crannies in your food bins and even eat through cardboard containers. Lurking roommates and so-called "friends" will devastate your supply of beer. Is there any way to stop the madness? To fend off the enemy? 
Also, even with the best of intentions, if you don't plan ahead for where all your cool new professional gear will go, you'll find yourself frustrated when you try to find what you're looking for. Do you put your hand in a kitchen drawer and pull it out to find several sharp objects attached? Is your medical kit getting low on supplies?* Ah, I believe we have identified a "need", here. THE NEED, THE NEED FOR.....uh, never mind.

Here I'll discuss a place for your Equipment, Ingredients, Plastic Storage for the closet and plastic storage for the refrigerator for your Left-Over Food, and then some basic Items for Cleaning. You'll find your life much easier when it comes to shopping, bringing home groceries, cooking, and clean-up. Not to mention you won't look like a slob and incur the wrath of your girlfriend, wife, or both. Or, worse yet, invoke the torment that is your mother.

A. EQUIPMENT

Pots and Pans

The most basic method is to have a few shelves near your stove and oven and arrange your stuff from most-used and most-accessible to least-used and least-accessible. Think about having to grab stuff while you're preparing and cooking and which cabinet is best to locate your items.
Another way to do this, and how I've done it in the past, is to buy a stack of restaurant-grade chrome open-wire shelving and just stack it openly there. You obviously need open wall space for your shelving, or this one's a no-go. The shelving is great because it gives your kitchen that professional look and the open wires don't hold dust.
The last way, but perhaps one of the most preferred, is to hang stuff from a pot hanger, attached to your ceiling. That's what you'll see in professional kitchens, so obviously there is alot of merit to this system of storage. The drawback is that you have to buy the pot hangar(which are sometimes pretty expensive), find room to install it(not workable in really small kitchens), and lastly install the thing. Not too bad of a project, but if you happen to be renting, you may want to look into what you'd have to do to repair the ceiling when you move. Along these same lines, you can consider hanging stuff on a wall next to your cooktop.

Knives

Unless you like explaining yourself to your health insurance company frequently, you'll need a good way to store all your knives. Not to mention that keeping them stored properly will prolong their useful lives.
If you only have a basic knife set of maybe a couple knives, then getting a magnetic knife holder will be perfect for you. You simply screw the thing into the wall next to your prep area and slap your knives onto the magnetic strip. If you've got kids, though, be careful where you place this.
If you do have, or plan to have, a larger set of knives, you'll need a quality knife block. You can either make one yourself(they're actually pretty easy to make) or buy a quality one from J.K. Adams or John Boos and Company.
Steaknives. If you opt for a knife block, consider getting one that holds your steak knives, too. Otherwise(and actually what I prefer), get a separate flat block that fits into a drawer.

Utensils

Now that you have all this professional gear, why in the world hide it? If you had a.......ah, skip that thought. I recommend you get several different utensil holders, which are basically open canisters. I have three: one, for whisks and flat spoons; two, for my spatulas; and three, for my wooden spoons. These are all kept on my windowsill in my kitchen, right by my prep area.
Now, also get some drawer organizers for a couple drawers. Think about your measuring cups, measuring spoons, etc. I hate to admit this, but leave one drawer open as your "junk" drawer..... invariably you'll have stuff that won't easily fit into a compartment or section of your drawer organizer.

B. INGREDIENTS

Dry Goods

You'll need some basic containers for bulk items like flour, rice, sugar, etc. Go to your local restaurant supply store and see what they carry.....you'll find they usually have some pretty good stuff at reasonable prices. Otherwise, there are plenty of reputable retailers that sell containers made for this.
For cereals and grains you use a bit more often, look at pop-top containers with a molded handle. I happen to like SnapWare containers.
Your potatoes and onions will need a dry place in your closet to hide. Either buy a basket for this, or you can buy a wooden box specially made for these items that is designed to sit openly in your kitchen. Somewhere.
Buy as many sealed GLASS, not plastic, containers for as many types of coffee whole bean as you think you'll buy. If you buy plastic, the gases in the beans will expand and crack your sealed plastic container. Yes, Brian, the beans give off gases. Ha ha.

Liquids

Most, if not all, of your liquids(vinegar, cooking wine, oils, etc) will come with their own bottles. Don't automatically throw these away when empty, however, as you can use them again to make your own vinegars, oils, and specialty cooking liquors. Otherwise, you can always go to crafts or home decor stores and buy new empty bottles.
For liquids like iced tea, Gatorade, etc you can easily find some pint and quart containers in any store.....keep a couple of each on hand.

Spices, herbs, etc.

Have a spice rack to store all your herbs and spices. You can also install a wire rack to the back of your closet door, which will maximize space. Better yet, install wire shelving in whatever kitchen closet space you have.....the epoxy-coated wire will last the longest.

C. PLASTIC

You'll want to have a bunch of different shapes and sizes of plastic containers to hold your cooking and leftovers. At some point, you'll have to decide whether you want to sprint for the really sweet FreshVac™ brand plastic containers, or go with the disposable plastic food containers that you can find at any grocery store.
And by the way, although I happen to like the quality of Tupperware and the fact that its supposed to be able to keep the Ebola virus contained from the average 2 year old chimp, its not only a bit overpriced, its also.....well, Tupperware. I have horrible visions of middle-aged housewives and waking up at 10 am, naked, drunk, confused, and with Tupperware all over my living room.

I really like the newest and best stuff on the market, which I just added to my store, FreshVac Pro™. They seal perfectly because they use a 100% silicon gasket.  The entire unit is stain and break resistant polycarbonate and you simply push down on the top and the thing seals with a one-way check valve.  Cool, huh?  I've got to say that of all the food containers on the market that I looked at, these are the most innovative and durable. Oh, that they come with a LIFETIME WARRANTY doesn't hurt either.

I admit I also kinda like the disposable containers easily found in any store, if for no other reason than they're cheap and totally replaceable (although dont' forget the FreshVac Pro™ comes with a Lifetime Warranty against breakage or staining. Theft you'll have to deal with your insurance company. Joy). There are several different brands out there; all decent. Downfall is that they don't seal as well and they usually stain easily and break if you rough handle them frozen. Also, another drawback is that they don't remove alot of the air inside the container, so your food won't typically stay as fresh as the FreshVac Pro™.

Now, not to miss anything, the last but perhaps most important part of this group is your zip lock bags, plastic wrap, and aluminum foil. Have some quart and gallon bags handy as well as a few Freezer sizes (you'll need the freezer ones for marinating as they generally seal better). Usually most plastic wraps are pretty good, and I keep forgetting which specific brand sucks, so we'll just leave it at that. Besides, it'll probably save me a lawsuit. Lastly, buy two sizes of aluminum foil: a roll of 12in wrap and, for big platters of large dead things, a roll of 18in aluminum foil.

D. CLEAN UP

Stuff

Cleaning isn't rocket science and you shouldn't have to have an advanced degree to figure out which of these crazy new "all-in-one" products to buy. Make it simple: 1)liquid detergent for general clean-up; 2)soft scrub for heavy duty jobs and stainless steel; 3)spray kitchen disinfectant, like Clorox Clean-Up.
For gear, I recommend 1)a small hand-held brush; 2)a sponge with a scrubber side; and 3)a plain scrubber pad for heavy jobs.
Oh, and have under the sink some natural non-aerosol spray air freshener, especially for the next day after your dog ate whatever you cooked last night.

Methodology

Some simple advice: clean as you go. That means, as you are cooking, keep cleaning whatever you're getting dirty. Keep up with it all along and you won't have a heaping load to take care of at the end of dinner.
Also, don't leave dishes in the sink. I'm not your mother or father, so I won't lecture you(thank God, eh?), but there are plenty good reasons to put stuff immediately in the dishwasher or to clean them by hand. Unless you're drunk and having a Tupperware party.

*And by the way, I actually wasn't kidding about having a medical kit handy, say with some band-aids, spray benzocaine, and anti-biotic ointment. Face it, my friend, you cook in the kitchen, you're going to get burned from time to time. Say ouch, move on.