This is by no means a comprehensive list, simply the top applications that I have found to be used nearly daily. In addition I'm not including utilities that ship with OS X. Without further adieu here is my take on them:
Though I also use Safari, my default browser is Firefox. Why? Extensions and add-ons. Firefox is effectively a mini-platform for web browsing and as a developer that builds web based applications the number of add-ons to help with HTML/CSS/etc. is mind numbing. The only problem I have with Firefox is that it needs to be restarted occasionally because it will suck up and continue to hold memory, especially after visiting Flash intensive sites. Since I rarely shut down my Mac Pro (I'll put it to sleep instead), Firefox needs a restart every 3-4 days. Example: As I write this Firefox has been up and running for 5 days and is currently consuming 508MB of memory. Fortunately there is an extension called QuickRestart that will allow you to restart Firefox and maintain all of your existing tabs and session states. Oh, and that extension is free too!
Though a relatively new addition to my collection of free utilities, Skitch has quickly risen on my list of must have, always handy utilities. As I wrote about it just last month, Skitch makes it so easy to capture, size, crop and annotate images that I don't feel at all compelled to fire up GIMP to edit my images. Add in the free storage and sharing capabilities from the Skitch online service and this is something you should have at the ready if you do ANY image editing or annotating.
Like Skitch, Dropbox is a relatively new addition to my collection of free utilities though I have found it an outstanding application and service. Why? If you have multiple computers you know that moving files between them can sometimes be a bit of a challenge, especially if you are going across platforms (Mac -> Windows -> Linux) like I do. Dropbox uses the web as an intermediary, effectively eliminating that issue. In addition I can detach my MacBook Pro from all networks—jumping on a plane for example—and my key files are there with me. When I return from my trip and reconnect to my network my updated files magically appear on my various desktop machines and even the VM Ware instance running Windows XP.
Rarely does a day go by that I am not consulting iStat menus to see what is up with my Macs, especially when I see inordinate memory usage (see Firefox above) or the CPU is taking a hit. iStat menu lets me quickly see what is going on and presents it in a seamless integration with my OS X shell. I got on the iStat menu bandwagon early in my Mac adoption and have been extremely happy with it ever since.
I'm online for the majority of my day and since I work from home I can't easily chat with some of my friends. Instant Messaging (IM) provides me with a virtual water cooler. As I have contracted out some of my development activities over the last year I've found IM to be a great way to quickly work through revisions and issues rather than pushing e-mails back and forth. I like Adium for this over iChat because it has a very compact interface and allows me to consolidate all of the various IM accounts (Google Talk, AIM, ICQ, etc) into a single place. Just a great all around application and one that I use throughout the day.
As an internet entrepreneur keeping up on the latest technology news is a bit of a challenge because of the sheer quantity. Though I've found sites like TechMeme very helpful for keeping abreast of what's going on I still like to rip through RSS feeds of my favorite sites to see what's up. NetNewsWire is great for this with a snappy interface and a built in browser that makes it easy to queue up stories to read while scanning the headlines.
I am a bit addicted to Twitter and have found the best way to manage my Twitter feeds is through TweetDeck, a wonderful little Adobe Air based application that presents multiple panes for each of my different views. Though I would prefer that TweetDeck was a native OS X application the developer for it has been pushing out updates pretty regularly and seems to be very attentive to requests from his increasing user base. In case you are interested you can follow me on Twitter by visiting twitter.com/dalison.
I haven't looked around too much for FTP clients because once I found Cyberduck I didn't see a need. My FTP requirements are generally very simple; push a few files up to one of my servers, grab a log file here or there, etc. For tasks like that it's hard to beat Cyberduck since I just fire it up and away I go, dragging and dropping files between Finder and Cyberduck windows as I need to.
I love Gmail; it's been very reliable, has plenty of storage, an excellent web interface and an IMAP connection that I can access nicely with Mail.app. The best way I've found to stay on top of incoming e-mails when I don't have Mail.app loaded is through Google Notifier. Sometimes the IMAP interface to Gmail can be a bit slow so Notifier gives me a quicker update when new mail comes in. An added bonus is that it also monitors your Google Calendars and can push out reminders for that as well.
Though I generally can watch video through QuickTime there are file formats that it can struggle with, even with some of the add-ons for it. If QuickTime can't play it I grab MPlayer OSX and it hasn't failed me yet. It's displaced VLC for me because the video quality seems to be a bit smoother.
So there you have it, my top 10 free Mac utilities. There are others that I use, just not as regularly as those listed above, including Handbrake, MySQL Tools,
One of the reasons I love writing these types of lists up is that I always get some fantastic recommendations for an application I wasn't aware of. Got a free application or utility that you really love and use all the time? Drop a note in the comments and share!
Update (3 Dec, 2016): I had listed TrueCrypt as a good free utility for encrypting data on your Mac. In the 7 years since this was posted TrueCrypt ceased to be in active development and has been found to have security issues. Several alternatives have surfaced that are worthy of considering, including VeraCrypt, which is based on the TrueCrypt code base but remains in active development. I have not used it yet so I cannot vouch for its capability.
I recommend checking out Paul Bischoff's post about free TrueCrypt alternatives. I rarely update older posts like this however anything where I was recommending products for personal security that have since been compromised will be updated.