First things first: Left-side Dock, forever. I know there are some people who prefer having their Dock along the bottom of the screen, but when you're rocking an 11-inch Air, a bottom Dock takes up valuable screen space.
And to borrow from the Doctor: side Docks are cool.
When it comes to the 11-inch Air, screen real estate is at a premium, so I tend to use multiple desktops in Spaces — each with their own desktop picture, naturally.
The one pictured above is my primary desktop (with a fun little Guardians/Star Wars mashup illustration from Matt Ferguson as my desktop picture). My other desktops have variations of the system wallpaper, for screenshot purposes.
I also use a ton of little menubarlet applications, most of which would go in my Dock if they weren't already hiding up in the menu bar. Those include Cloud for quick uploads; Knock for remote Mac unlock; 1Password for all my passwords; Fantastical for quick calendaring; Dropbox for file storage; and CloudClip for wirelessly syncing my clipboard between my Macs and iOS devices.
My MacBook Air Dock itself is organized into the following sections: Web, Writing, Communication, Photos, eBooks, and Music. I've got plenty of other apps I'll launch from either the menu bar or Spotlight, but these are the ones I use most often (and also the ones I find myself dragging files to fairly regularly).
I have both Safari and Chrome at the ready to accomplish different Web-surfing tasks: Safari is my browser of choice for most day-to-day activities, while I use Chrome for Google Hangout meetings and any other work-related multimedia. (YouTube, Dropbox, et cetera.)
On the writing side, BBEdit takes the crown: I've used many Markdown-inspired text editors, but I always come back to BBEdit. It's smooth, smart, and its Dropbox sync between computers is excellent.
Mail, Slack, Messages, Skype, and Tweetbot make up my communications suite. I've tried several third-party email clients, but as of yet haven't found any I like as much as Mail. (Airmail isn't bad, though.) Slack is iMore's central chatroom, while Messages, Skype, and Tweetbot get used for work as well as roller derby, The Incomparable, and more. I can't say I'm thrilled with Skype — is anyone? — but it does what I need it to do for now. Tweetbot is my go-to Twitter client for both my personal Twitter account as well as management of the iMore twitter account.
I rely on Napkin, Pixelmator, and Photoshop for all my iMore-related screenshot and photography-editing needs — and a little bit for my personal use, too. I've had a long history with Photoshop, but I'm trying to use Pixelmator more and more as my primary image editor. Its Handoff support with iOS devices is excellent, and it's a real selling point for me at present.
Next we've got my ebook tools suite, currently iBooks Author and Vellum. I use iBooks Author for when we want multimedia content and widgets in our ebooks, while Vellum is my all-purpose tool for working on our cross-platform versions.
Finally, iTunes lurks at the bottom, like the lurking lurker it is. I'd like to take iTunes out of my dock, but I still use it a bit too much to do so. I stream my music library via iTunes Match to my 11-inch MacBook Air to save space, and iTunes is currently the only way I can do that. I do often listen to Beats Music, but there's no dedicated app for that; instead, I open up a Chrome window.