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In the computer field, "religion" is a technical term that refers to the usually irrational and extreme preference of one program, style, or method to another. Although you cannot really do anything about this phenomenon, you can keep it in mind when analyzing comments on your design.
It has been observed that people often "get religion" over the first application (for example, a word processor) that they use. I can't recall the number of people who have tried to convince me that the program that they just discovered (i.e., the first one they used) is the best one in the world. This form of "religion" is normal and derives from the facts that (1) the move from manual to automated methods (e.g., from typewriters to word processors) involves a major increase in capabilities: even the simplest word processor provides vastly more capabilities than does a typewriter, and (2) new users do not have the experience to realize that all programs (e.g., word processors) are not equal. This form of religion usually fades away over time as new users gain experience.
In a hauntingly close parallel to the "second system effect" (Brooks 1982), the "second program users" are the ones to watch out for. These people started using one program, then gave that program up in favor of a second one. The problem is that they think that since the second program is better than the first one (which it usually is), it must therefore be better than all the rest.
There is nothing in particular that you can do about users that feel religious about a program: rational arguments are in general ignored. You can, however, be aware that such users exist, and recognize when you are dealing with one.