When you love Dropbox like we do, you start syncing more and more stuff. The more stuff you sync, the harder it is to organize. Here's a simple way to sort quickly and stay organized across multiple computers, Windows, Mac, or Linux.
We're going to deal with two things here: organization and synchronization. Organization is the big part, since that relies mostly on you (whereas synchronization relies almost entirely on Dropbox). We'll tackle organization first, then take a look at some of the issues you may encounter when syncing almost everything you do on your computer. While I came up with these organizational ideas using Dropbox, many could apply universally to any modern file system. Some will require Dropbox, but you can still use most of these organizational ideas without it.

The Structure

Dropbox starts you off with a bunch of folders, and rather than change a bunch of things we're going to keep organized by building on that. Before we dive in, let's take a look at the folders you'll want to have in your Dropbox. Once you have those, we'll discuss how to use them.

• The Dump
• The Landfill
• Projects
• Documents
• Your Flex Folder
• Applications
• Movies
• Music
• Photos
• Shared Folders

Alright, let's get started!
Ed. note: If, after consideration, Adam's folder structure doesn't feel right to you, you may also want to consider Gina's My Documents organization structure.

The Dump and the Landfill

We are not perfect. Like many diets, organizational systems expect us to simple curb our flaws for the sake of bettering ourselves. You've got a limited supply of willpower, so how you organize should recognize that. The Dump is all about having a place for your imperfections. You need to have a work folder where you can just save things arbitrarily. Starting on the first day of your week, everything you're creating gets saved to The Dump. It doesn't matter what kind of file it is or what kind of project it's for—if it belongs to the current work week, it belongs in The Dump. If you take lots of screenshots, change the location of those screenshots to The Dump (here's how to do it with OS X's default screengrab). Whatever you create and whatever assets you use to create it, make sure this is where they go first.
When you reach the end of your work week, it's time to organize. You should only need to set aside about 15-20 minutes to go through The Dump and decide what to do with everything. This week I ended up with 145 items and was able to sort them in about ten minutes, so don't worry about how long that list of files get. If you start by listing everything in The Dump by file type you can start cutting the fat more easily.
First go through and find things you've saved to The Dump that you no longer need and delete them. Next, select the files you're not quite ready to throw away and put them in the folder called The Landfill. The Landfill exists so you don't have to spend time deliberating over whether or not you need to keep certain files, and if you do, where to put them. Once a month you'll need to spend some time cleaning out The Landfill, but a month away from most of your "maybe" files will give you better perspective on whether or not you need to file them or throw them away. Most of the files in The Dump will either end up deleted or buried in The Landfill at the end of the work week. Once you've gotten through those, you'll find you have a handful of other files that should only take you a few minutes to sort. Sort those and The Dump is ready to go for next week.
These two folders—The Dump and The Landfill—will be the most important part of how you keep things organized in your Dropbox because they allow you to be a little lazy, but it's important to not just let everything flow or you'll become overwhelmed as it gets later in the work week. When you're working on something new, even if you think it might only require a file or two, make a new folder inside of The Dump to contain it. Do not make efforts to spend time organizing the dump, but definitely take a second to keep similar files together so you can move through The Dump quickly while you're working.

Projects and Documents

Projects and Documents are where you'll end up keeping most of your work. Projects should be made up of active projects you're working on. You can just keep individual project folders inside (e.g., New Rock Ballad, Essay About Strawberries, Johnson Wedding Photos for Album, etc.) or create a sub-structure of project types if you do a lot of different things (e.g. Audio Projects, Video Projects, Photo Projects). The important thing is that this folder only contains files for long-term projects you are actively working on (as in things outside of the scope of the current work week, as those files are relegated to The Dump). I find it helps to keep my to-do list in here as well. I use an awesome Mac application called TaskPaper and save my project to-do list in the root of the Projects folder. You can use whatever you want for your to-dos, but if you need to save a physical file somewhere the Projects folder is a great place to put it.
Where Projects is your active work folder, Documents is your dormant work folder. Consider Documents useful for two things: static documents you may want to reference or use more than once (like stock photos, forms, etc.) and finished projects you want to archive from your Projects folder. Organize Documents however you like, but don't put anything in it that you're going to change. While the Projects and Documents labels work well for me, you'd have a good point if you argued they're not intuitive. The labels Active and Archive might work a little better for some, but choose what's right for you. As with everything described here, this is an organizational idea, not a paradigm. There really are no paradigms—only systems that work for you and systems that don't.

Your Flex Folder

Being that there is no such thing as an organizational paradigm, no system broad system like this can account for your specific needs unless it provides that kind of flexibility. This is where your Flex Folder comes in. Chances are you have something in your life that just needs to exist outside of the big buckets that make up most of your Dropbox. For me, it's a folder called Writing. I love to write, and so it doesn't stop with Lifehacker posts. I write short stories, screenplays, ideas, or really anything I'm in the mood to write. This adds up quickly and I've found it helps to have it all in one place, separate from all the other stuff that I'm doing. As a result, my flex folder is a dedicated Writing folder.
The reason this is necessary is because my Flex Folder is sort of a combination between active projects and archived documents. Everything I save into my Writing folder could end up staying there untouched indefinitely or could be very active. The problem is, I don't know which category each piece of writing will fall under. As a result, having a Flex Folder for writing lets me organize these documents with that extra flexibility. If you do any kind of work that doesn't allow you to apply the active/archive structure, a Flex Folder is often the answer.

Applications

Because we're syncing all of these folders between multiple computers, it's easy to end up with a machine that requires a certain Application that isn't installed. While it's not that hard to download what you need online, it's annoying to have to stop your work to search for the application you need, wait for it to download, and then getting back to work. If you're focused and in the zone, you want to minimize these problems as much as possible. Keeping installers for commonly used applications (or even portable applications that you're running directly from your Dropbox folder) in a synchronized folder will help you do that. While you're not going to keep big installers in here (like Photoshop, for example), it's a great place for smaller installers for those applications and utilities you can't live without. As an added bonus, if you ever need to share an app with a friend you can do that directly from your Dropbox.

Movies, Music, and Photos

If you're using a free Dropbox account and surviving by referrals, chances are you're not going to have enough space to sync your rich media. If you're paying for an account of 50GB or more, however, Dropbox can do a great job of handling your media. (Dropbox offers a 50GB plan for $100/year and a 100GB plan for $200/year.)
Movies and photos are both pretty simple, since they can be organized in similar ways. About a year ago I got fed up with iPhoto and decided to try something else. That something else was an organized folder structure for my photos, forgoing any actual application to help me out. Dropbox made for a perfect partner because it provided an automatic backup of all my images. I have an enormous photo collection, but organizing it wasn't all that hard because you really just have to look your Photos folder the same way you'd look at managing your photos in a photo management application: organized by albums. The problem is that a directory isn't ordered any way you want it, but rather based on certain criteria. Generally you're going to organize your files in alphabetical order. To ensure similar albums stayed together, you can just add a tag to the front of the folder name. For events, I added a date stamp (e.g., 2008-09-21). For portraits of people, I added the tag PEOPLE. Folders containing wallpaper were prepended with WALLPAPER. The idea is pretty basic but it helps keep everything sorted nicely. This same method works well for movie clips, too.
Music gets a little tougher because many of us use iTunes, or something like it, to work with our music. The problem with syncing iTunes with Dropbox is not so much keeping files in sync but keeping your iTunes Library file in sync. If you have iTunes open on more than one machine at a time, you'll run into problems. While there are other ways to go about it, one of the easiest solutions is to also use iTunes syncing software like MediaRover that will handle the synchronization of your iTunes Library file so Dropbox doesn't get confused. Alternatively you can just be diligent and make sure you always close iTunes when you're finished so it never ends up being a problem, but this is requires a lot of you and can be a dangerous road to follow. Unless your music player doesn't use a database file or you just don't use one at all, syncing your music with Dropbox might be a little more work than you're willing to do. This is one task you might want to set aside until a simple option comes along.

Shared Folders

Dropbox's shared folders feature is really great—especially if you need an alternative to the now defunction Drop.io—but as soon as you start sharing a bunch of folders with people it can get tough to manage. The solution is very simple: put all of your shared folders in one place. This may seem a little obvious, but it's something you want to get in the habit of doing before they start piling up. It's great to be able to easily share files with coworkers, friends, and family, but when they clutter up your Dropbox or get lost in your organizational structure they end up being more trouble than benefit. Get on top of he problem with a single location for shared folders and you won't have the problem at all.

Customize and Be Flexible

I deal with more files (and different types of files) than the average person, and this is a system that's worked really well for me. It's about as ideal and perfect as I could possibly ask for and it makes my life easier every day. That said, you're not me. You do different things, have different talents and flaws, and could be a very different person. If you want to implement this system, the first thing you should do is assess any doubts you might have. Chances are most of these ideas can help you stay organized and productive across your multiple computers, but only if you put a lot of yourself into the way you implement them. This setup may not work for you exactly as is, but try it out in a way that suits your needs best.