When it comes to the iPhone, it's really really difficult to narrow my app love down to just three picks. So with apologies in advance for all those amazing applications that didn't make this cut, let me jump in with three choices that I simply do not live without on my (jailbroken) iPhone:
Cydia. When Jay Freeman's Cydia first debuted, I was hesitant to use it. It sucked up the root partition space like a sponge and its interface was, at best, preliminary. And now, in 2.0, Cydia owns me. It's simply fabulous. From its command-line Unix support to its fully overhauled interface to its extremely workable update system, Cydia provides a powerful software distribution system, perfect for modern smartphones and a great competitor to AppStore.
Boss Prefs. Boss Prefs offers a wonderful services application. It lets me enable and disable services such as EDGE, Bluetooth and SSH from a central application. Because I only intermittently subscribe to data plans, Boss Prefs ensures that I won't accidentally start downloading a la carte data that starts at about $500 million (or so) per kilobyte. It also lets me enable and disable my mail accounts, so the iPhone works perfectly for whichever mode I'm in: intrepid TUAW blogger at large or private Soccer Mom on the go.
Othello. Othello is my current fidget-game-on-the-go. When I'm stuck waiting somewhere for a few minutes, I pull out Hongtao Guo's perfect take on Othello. With three playing levels, optional sound and a really nicely designed interface, Othello provides the perfect time waster. There are other free versions of Othello under various names on AppStore but I particularly like this implementation. Although I wish it would put me directly into the game board rather than the welcome screen, that's my only criticism of a lovely, free application that's a great deal of fun.