If the biggest concern is that users won't realize that they may not be able to use a .NET app on any computer, couldn't we standardize some sort of warning in the first sentence of the description? For instance:
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WriteMonkey requires .NET 2.0 or higher, and provides a distraction-free writing environment.
I realize that this may have the effect of driving away a couple of purists. However, if they won't visit a database of portable applications because it's tainted by a handful of programs that require .NET, that seems more like their problem than ours.