In-house programming doesn't need to be as bad as Joel's experience. Yes, you are in what is called a "cost center" that doesn't get the same management priority as a "revenue center." But the more closely your work is aligned with a revenue center, the better treatment you'll get.

In a software company, you're in a revenue center. The problem is that you may have to sign a draconian intellectual property agreement, jeopardizing side projects. This is less likely as an in-house programmer.