Handy as citizens are, you shouldn't raise too many — train up only as many as you need to staff any economic buildings or construction projects as you may need, like the construction of a Wonder or a new Fort, otherwise you run the risk of wasting your Food and Population on units that actually don't do anything for your cause.
Guard your Citizens well, for having a healthy population dragging in resources can spell the difference between victory and defeat. Should the mass of your Citizens be massacred late in the game, then defeat is sure to follow. Either you will not have sufficient resources to defend your nation, or your enemy will out-boom you, obtaining either a Territory or a Wonder victory in no time.
On the other hand, should you have too many Citizens, or a desperate need for units to defend your homes, then consider researching the Militia upgrade from any one of your Tower-type buildings. This will increase the offensive power of your Citizens, making them far more useful even if only as a meat shield. You can then use these Citizens to either draw fire from your enemy's units, or otherwise send them in to finish off a weakened foe.