Resetting application window size

I would like to know how to reset a user set window size for an application to the one chosen by the developer. Are these settings usually stored in some plist file?

It depends on the Application, but mostly it's stored in the defaults database. You can check for example Mail.app with:

defaults read com.apple.mail DefaultWindowState

If You do not know the key just grep with "window" the output from defaults read BUNDLE_ID where BUNDLE_ID is Your application bundle identifier which can be read like this:

APP_PATH="/Applications/Mail.app"
defaults read "$APP_PATH/Contents/Info.plist" CFBundleIdentifier

You can try to change keys in plists using defaults command or locate plist file in ~/Library/Preferences directory and change it manually.