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It might be nice if at least the command-line tools (plink et al) could honour the commonly used environment variables http_proxy, ftp_proxy, no_proxy (etc?), using them to automatically configure use of PuTTY's HTTP proxy features.
Of course, there would have to be some obvious and easy way to override this, because in many circumstances it wouldn't be The Right Thing to do.
I'm not sure whether there are written standards for the names and contents of these variables anywhere or whether they're just defined by common practice. Ben suggests that NCSA Mosaic might be a good place to look.
Audit trail for this wish.