By managing two different teams at the Apple developer site, I’ve been able to compare iOS developer programs over time. The $99 individual and company programs are an OK first step, but you get what you pay for. With these programs, ad-hoc (pre-store) distributions are limited to 100 devices, each of which must be registered. And every new device registration requires updating provisioning profiles, refreshing, and repackaging. This also makes testing at cloud services like DeviceAnywhere a major hassle.
With the $299 enterprise program, you can get that magical ProvisionsAllDevices in your embedded.mobileprovision and get out of the device registration business. Unless you’re only distributing internally to a very small team, the $200 shakedown is well worth paying for.
Of course, when it’s time to submit to the store, you must use the non-enterprise membership, so that $99 company membership isn’t wasted.