Martin,
One of the things that has bugged me a bit is that when using the Include Mask to upload files, it only works in the current directory (unless I've missed something).
It would be nice if WinSCP would either recurse directories when using the include mask by default or accept "//*something.ext*" as an include mask and recurse directories (double slash is xPath lingo for wildcard directory/path selection).
Thanks
~duerra