Runes may be of any charge. Ie, they can be set to half power, twice power, etc. Custom, graphical server-config menus. These are randomly spawned throughout the level. Adjustable bonuses given to capturers, defenders, assisters, and flag-carrier frags.
Custom skins and flag model.
In-game dynamic music. Different music is played for each player depending on their team's flag status and whether or not their, or some other team's flag is out of base. Team-Oriented shield belts. I.e., Red players get a red shield belt, blue players get a blue shield belt, etc. And of course, all the source is open for others to use, provided credit is given where due.