Resetting application window size
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.