First off let me state that I run my roads through my cities. I know some Civ (maybe CivII?) players got in the habit of running their roads around their cities because the city tile always showed up as a "road". This meant that you lost a third of a movement point when the unit travelled through the city, even though all the surrounding tiles were set to railroad (think of maglev). Unfortunately, the opposing civs used this to their advantage and could quickly use your infrastructure to move their units to weak cities quickly.

Since I run my roads through my cities, I run in to a different kind of problem. I can't move big armies to the front quickly. So I have standardized on creating armies of 10 units, and only having two units in the city as defense. This speeds up my wars considerably, since I am able to use my infrastructure to move my units around.

Of course, if a city is in jepordy, or that city is not a common thoroughfare, then beef it up. But if it is a city that units pass through all the time, follow the ten and two rule.

In the late game (in CTP1), when I've got nothing but War Walkers moving around, I'll usually march them around in groups of 3-5 in enemy territory. Move a bit, then bombard; and if the city seems to be weak enough, maybe capture it next turn.