Add in that they may be using these custom apps to handle medical data, or financial data, or something similar that can cost lives or staggering sums of money if a browser upgrade causes even subtle errors... so there's a time-consuming and very costly certification process that must happen even for rewritten software, on top of the cost of development.

And certification would need to happen again before any subsequent browser upgrades.

So I hate supporting IE6, but I'm working in health care, so I'm pretty sure that I'm going to be supporting IE6 for a while yet.