Starting with the recent beta releases of the iPhoneOS, Apple has started requiring that all code on the device is signed. This is mostly to make it impossible for programs running through Apple's AppStore to download more software and run it (so no competition for AppStore).

In order to get around this (and thereby to install our own code onto the device) the iPhone Dev Team has patched the signature verification out of the kernel. However, another half of the codesign problem is that the binary contains a number of SHA1 verification hashes that are checked in numerous locations throughout the kernel. Patching this out is A) difficult (especially to track as Apple makes changes) and B) of marginal benefit as adding these hashes is easy. This means you do still have to at least pay lipservice to the code signature process. There are currently three viable options.

Option #1: Self-Signing

This method is the simplest to understand: using Apple's codesign tool to sign the binary. Because the signature verification checks have been hacked out of the kernel, you can use any signature to do this, not just ones that are approved by Apple's developer program. For instructions on how to make a self-signing certificate you can read this article from Apple's website: Obtaining a Signing Identity.

from your Desktop Macintosh

codesign -fs "Name" Program
scp Program mobile@iphone:

Option #2: Pseudo-Signing

For me, the previous option just doesn't work. I do not use Macs to do my development and the entire codesign path requires not only a Mac but console access because codesign is, at some level, a graphical utility (the way it uses Keychain to get the signatures may prompt, with dialogs, for passwords). To get around this, I wrote a tool called ldid that, among other things, can generate the SHA1 hashes that are checked by Apple's iPhoneOS kernel. This tool is easily installed on the iPhone using Cydia or APT.

from your iPhone Terminal

apt-get install ldid
scp user@desktop:Program .
ldid -S Program

Option #3: Disable Checks

Finally, an option that is really convenient for development purposes is just to disable the check. Now, technically, this disables a lot more than just the codesign check, and its also more disabling the penalty than the check itself. I have run my phone for a while in this state, but I have heard that in some (many?) configurations it causes problems: being unable to connect to insecure WiFi networks being the largest. This is done by using sysctl to deactivate the enforcement and can be undone either by resetting the variables back on or by rebooting the phone.

from your iPhone Terminal

sysctl -w

(to undo, either use =1's or reboot)