-= Existing System =-
Currently, the clan system is nothing more than another chat channel.
-= Clan Castle (Fortress) =-
I remember the clan system used to have a clan castle and I think it would be great to put it back in. The defense of the fortress would be determined by the total overall levels of the clan. This would not only affect the level of the guards, but also the type of guards (mages,fighters,clerics,etc).
Next, there should also be purchasable enhancements like warning alarms, tougher doors, fountains, teleport runes, npc shops, etc. These enhancements would have a monthly upkeep cost that can be paid up to four months in advance. This money would be stored in the clan treasury (That can be lootable by non-clan members). If the money in the treasury runs out, the enhancements would also disappear.
This is just a start, but I welcome any more ideas, suggestions, comments, whatever...