A couple of years ago I wrote a post outlining many of the tools we are using to run the business, work with clients and build websites. Of course a lot has changed since then. I'm always interested in what others are using, so hopefully some of you folks can benefit from this updated list.

By far my favorite app, the one that's most crucial to our work every day, is Dropbox. It stores all my files securely online, keeps backups and previous versions automatically, syncs everything across computers and even on my iPhone, allows me to share files and folders with my partners and does it all incredibly well without getting in the way.
Utilities
1Password (Mac/iPhone/Browser Plug-ins)
1Password is a useful application for keeping track of your logins/passwords. It makes great use of browser plug-ins to add new logins and sign you in quickly to sites it knows about.
This SSB (site-specific browser) allows you to use web apps like desktop apps, giving them a separate icon in your applications folder so it works independently of other apps. It's great to use for your favorite web apps.
This is the best document scanner you will ever own. It's so awesome that I got the small version for home and highly recommend both.
This app is incredibly useful when you need to find a hex value fast.
Very handy application for taking photos and videos of your screen
Creative
Sharpie and Paper
All our wireframes start with a blank sheet of paper and a sharpie! I recommend the Dot Grid Book for sketching.
I create sitemaps using OmniGraffle, and sometimes wireframes if the project demands it. However, we prefer not to get more specific than the paper/sharpie method whenever possible.
We use Fireworks, Illustrator, InDesign, Photoshop and the Media Encoder regularly.
Code
Text editor that's fantastic for coding, and I also prefer to blog/write using it
I recently started using this super cool bundle that makes writing HTML and CSS 100% faster using abbreviations and snippets. This article should get you started.
This is a free tool for comparing files and finding differences between the them.
Great FTP client, easy and reliable
Beautifully designed subversion client, love it
Communication
Great little open source instant messaging client that supports any well-known provider (AIM, Yahoo, gTalk, etc.)
Skype (Mac/PC/iPhone)
Skype is a swell app for VOIP phone calls and chat
They are not perfect, but I prefer the default OSX tools for email, calendar and contacts. I especially love the Letterbox Plug-in for mail.
CoTweet is great for companies that have numerous people managing one twitter account.
Great twitter client, beautiful UI for both the Mac and iPhone
We use this as a conference call number and also for client demos of all sorts.
This is a nice little application to schedule tweets for the future.
Productivity
I store all kinds of notes in this program, along with categorized bookmarks. If I don't know of a place to put or remember something, it goes in Evernote.
EVERY task goes through this app, as I swear by the GTD methodology.
Great paper tool for taking notes in meetings and so forth
Financial
All our time tracking and invoicing takes place in this app. The clincher for us is creative control over the template design using HTML/CSS.
Quickbooks 2008 (Windows)
I'm looking for a reason to ditch Quickbooks, so I am not going to link it up here. It's just tough to find a system that is CPA-friendly and has the advanced features we use.
All recurring and credit/debit card billing goes through this system. It's primarily built for hosting providers, but we know the developers of this software and enjoy using it.
Firefox Plug-ins
THE web developer tool of choice!
Great firebug extension that helps developers optimize pages for speed, according to Yahoo's best practices
Another firebug extension that is great for optimizing and measuring web page loading time
If you use Google Reader, Feedly is a sweet little tool that structures your feeds more like a newspaper. Sometimes I prefer using this instead of the reader interface. Cool idea!
Simple little tool to measure the pixels on a web page
Neat tool for taking a full page screenshot, no matter how long the web page is
Sync your bookmarks across browsers and computers, or even view them online
Lots of very useful tools for analyzing and building websites
Website Optimization and Monitoring
This is a truly awesome tool where you can watch videos of people using your website and see very useful analytics. It's a great form of user testing because it is cheap and users don't know they are being monitored.
A great way to visualize how visitors are interacting with individual pages on your website
Comprehensive tool for doing A/B or multi-variate testing on your website
Definitely the most popular analytics platform, and you can't argue with the price
Uptime and performance monitoring, which notifies us immediately via email and/or SMS the moment anything is funky on one of our servers
Our team created Linkpatch, and we use it to watch for broken links on our websites. If someone encounters a broken link on the website, we get an email with all the information necessary to fix the problem.
Other Apps
We recommend this service to ALL our clients for email newsletters and marketing, they rock
Really useful feed reader
We created Feed My Inbox, which you can use to subscribe via email to any feed. It's very handy for people that don't use feed readers and want an easy way to follow their favorite sites.
I've never owned a fax machine, so this application gives me a number by which I can easily send/receive faxes via email.
My very favorite way to conduct online surveys
Tripit (Web App/iPhone)
Automatically organizes your trip itenerary