1Password - This password manager uses a single strong password to encrypt a database of all your other passwords. Using this database you can find all your weak passwords and change them to stronger passwords, log into websites using a keyboard shortcut (⌘+\ on Mac) and your master password and more. This is one of the few apps I use multiple times a day.
Dropbox (affiliate link) - Dropbox saves my sanity weekly. It creates a simple folder on your desktop computer that is synced with the cloud. This allows you to share these documents between your devices and with others. You get 2 GB of free storage and an extra 500 MB if you use my affiliate link.
Backblaze (affiliate link) - Simple, fast online Back-up. We each get one month free if you sign-up using my link.
Mint - This service makes some people nervous, but it pulls data from almost all of my financial accounts and allows me to run analyses and get alerts on my usage. This has really helped me simplify my budgeting and stay on top of where my money goes.
Waze - A great cross platform social GPS app. It brings in accident reports and police spottings from other uses and warns you. It can even help to reroute you based on user input.
F.lux - makes screen more yellow in the evenings, easier on eyes and sleep cycle
TextExpander - This is like steroids for your text usage. From something as simple as correcting commonly misspelled words to letting your type a 2-4 characters and getting your entire address or a canned email, if you use text a lot you will love this app.
Alfred - Another app I use daily, this app lets you bring up a search with a keyboard shortcut (mine is ⌘+Space) and lets you do everything from search Google, to opening a document to launching an app. It really makes the dock and desktop shortcuts obsolete for me.
Bartender - I thought this app was gimmicky at first, but I have come to love it. It allows you to rearrange your menu bar icons how ever you like. In addition it give you a "second" menu bar to hide those icons that you like to have but do not want to see very often. It has really helped me clean up my menu bar and make it more legible.
Fantastical - Using real language (like "Coffee with John at 7) it will create calendar events. What more could you ask for?
AirServer - This app turns your mac into an AirPlay server, allowing you to send music and video from your iOS device to your mac. This is great if you have nice speakers hooked up to your mac and want to listen to media that is only on your iPhone. It also is great for practicing presentations and such.
Notational Velocity - Fast and easy note taking. Has the option to sync with Simple Note or Dropbox
Caffeine - Keeps screen from going to screen saver or dimming, good for watching videos
Spirited Away - Auto hides windows not in focus
Drafts - If TextExpander for Mac is steroids for text usage, this is the same thing for iOS. TextExpander Touch integration has to be implemented by each app developer, but Drafts lets you use TextExpander and normal text and send them to many apps across the system even if the app does not support TextExpander on its own.
Launch Center Pro - Allow you to quickly launch applications and even send data to those applications. This is a nerdy tool, but I love it.
Dark Sky - If you want to know when it will rain near you, this app is scarily accurate. It is not 100%, but usually in the ball park and makes me feel like I am in the future.
AirFile - Do you use Dropbox, Google Drive, Sky Drive, FTP and or more cloud based document storage systems? This app lets you move documents in and between all of these systems easily.
Sleep Cycle - Uses your movement in bed to estimate and track sleep quality. Really cool little app.
Overcast - My current podcast app of choice.
NameCheap - My domain registrar of choice. Good prices and nothing sleazy.
SquareSpace - This site is on SquareSpace and I have enjoyed using it.
GitHub - This is a version control system, hard to explain in a small space, but if that sounds interesting check it out.
Rackspace Email - $2/email/month ($10/month minimum). Good price and a great service. I love that I have people that I can actually talk to if I run into issues! Plus no ads! And if Exchange is your thing they can do that too.