You can also configure wine just by editing the wine.conf (or was it wine.cnf ?) file that should reside somewhere under your home directory (~/.wine/wine.conf ?). It's a "text file" so just use your favourite text editor. Also read the man-pages of wine if you need any information about the file (though it's quite straightforward).
Winecfg is, as far as I know, just an automated way of altering the file -- so you don't have to write content to the file yourself, but the app "asks" you the options.
EDIT: also, by editing the file by hand, you'll probably get more choices than using the config app.
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