iBlacklist: If you're tired of getting repeated calls from persistent telemarketers or you just don't feel like talking to that certain someone, iBlacklist allows you to automatically block calls, either sending callers on your blacklist to voicemail, giving them a busy signal, or just ending the call. You can also set up whitelists to only allow specified numbers to reach you or set up different behaviors for different days of the week. The amount of customization is actually quite impressive; it's clear a great deal of work went into creating iBlacklist before it was quietly blacklisted by Apple.
PDANet: While AT&T continues to delay the rollout of tethering (not to mention MMS!) and various rumors have been flying around regarding the cost of the service, us jailbreakers have been happily tethering for months. PDANet is easy to use and free to download. Just set up an ad-hoc network on your laptop, connect to it via your iPhone's Wi-Fi settings, start up PDANet, and you'll be clipping along on your laptop at vaguely tolerable 3G speeds.
Five Icon Dock: Not an app, per se, Five Icon Dock is a hack that can be obtained and installed through Cydia that does exactly what it sounds like: fits even more stuff right down there. Before Five Icon Dock, I was constantly faced with the dilemma of whether I needed Safari or Maps at my most immediate disposal, but now I can have my cake and eat it too!
Swaptunes: This little app lets you sync your music to two different iTunes libraries. Obviously this feature was omitted and this app denied from the App Store as an attempt to battle piracy, but there are also perfectly legitimate reasons to have two different machines with two different music libraries: home computer, work computer perhaps?
MXTube: Finally, a way to watch YouTube videos offline! MXTube allows you to download YouTube videos to your mobile device for viewing on the subway, plane, or in those pesky dead zones. Functionally, it works similarly to downloading podcasts from the iTunes store and even allows background downloading.