This distinction is a very important one. It's one of the big questions we work on with startups building stuff that's ultimately intended for business users: do you come in through the official channels, or force your way in via rebellious users? All other things being equal, I tend to prefer the latter, because (a) it's cheaper, and (b) it causes you to focus on building something great, which is a clearer and more reliable test than pandering to big companies' present taste in technology.

Amen -- as someone who has sold startup software the "official" way, the back door is definitely better.

It limits the possibilities of what you can offer, though, if your product needs proprietary or "difficult to obtain" data (i.e., data that the actual user can only get through one of his I.T. support guys).