Substrate version 0.9.5000 is now compatible with both iOS 7 and the ARM64 CPU used in the iPhone 5S (and many of those new iPads).

In the course of obtaining full access to finding private symbols on iOS 6.x, version 0.9.4000 apparently became incompatible with all hacks similar to Spire. This has been fixed in 0.9.4001.

As of version 0.9.3997, you can now disable Substrate entirely by holding down Volume Up as the device boots.

This feature allows you to bypass horribly broken extensions (ones that prevent the device from starting up at all) that you may have installed so you can open Cydia and uninstall them.

To support devices that do not have a Volume Up button (the first-generation iPod touch), you can alternatively hold down the "Clicker" (not Volume Up) button on your headset or earphones.

(A special thanks goes to @oLunatiko for help implementing this feature!)

As of version 0.9.3993, installing and upgrading MobileSubstrate no longer requires rebooting your device, ever.

Substrate is also now compatible with the idea of a "semi-tethered" jailbreak.

Finally, developers can now hook almost any daemon without having to request their inclusion with saurik.

Mobile Safe Mode is a feature designed to protect you from faulty extensions (it is pretty awesome).

Support framework used by iPhone projects such as WinterBoard, Activator, and Five Icon Dock.

The general idea is that there are a number of reasons one might want to hook functionality into an existing application. In order to do this there are a few dangerous or complex steps. By centralizing the code for these we can hope to get them right.

As an example, MobileSubstrate provides a simple platform (one integrated with Cydia) for deploying code that gets inserted into graphical applications. When things fail, it is able to provide error handling and fallback support (think of a "Safe Mode").