We use it all the time for process risk assessments - we use MindJet's MindManager software. It's a great way to effectively brainstorm variables that impact our chemical processes. And with the little +/- toggles, one can easily drill down deeper and deeper into sub-elements of variables or pull back out to get the high level view.
We then have a macro that some smart kid wrote a few years ago to extract all the possible variables that might influence a process step from the mind map and put them into a nice Excel spreadsheet for the next step in the risk assessment process. That is, ranking the risks to process success associated with each variable, which then leads to an overall risk ranking for each variable, which then provides us numerically ranked priorities for which experiments to run.
It's a little extra work, but the experimental plans we develop are more comprehensive and much less likely to overlook important variables that might be missed by just doing it by instinct. I've seen mindmaps used elsewhere at work, also.
