Build ports everywhere as soon as you can. For me this seems to be the main source of income. I also upgrade roads as fast as possible since these provide a significant movement bonus allowing better shuffling of armies. I tend to build defense and training facilities based on regions. For instance, Italy is a region for me, as is Gaul, Britain, Spain, Greece, etc. Each of these areas must meet some basic requirements for me. First, there must be at least one standing army in each area to deal with rebels and potential threats. The more remote and less threatened, the weaker and older this army can be. In more hostile areas, it must be reinforced and upgraded more often. In addition, border cities I usually upgrade to stone walls because of the significant increase in protection these give. Back-area cities only get wooden walls. In addition, I try to specify one or maybe two cities in each region as the unit-production facilities. They don't need to be able to produce the top-of-the-line units, but something good enough to hold off the masses until the main armies arrive.

Italy is an exception to this for me. Italy I upgrade every city so that I can spit out many units per turn and quickly assemble new armies to distribute to the threatened regions of the empire. This is the perfect spot for this since it is essentially central to every area of the map. I'm sure the tactics are different for other factions, but for the Romans I produce 90% infantry (Hastatii, Principes, Cohorts, whatever your best is). Missile troops I mainly use on defense and bridge defense with maybe 1-4 cavalry units per army. As such, all my Italian cities can produce the best infantry units they can, with one or two cities each that can make good cavalry, missiles, and siege engines. The infantry steamroller seems to work very well for the Romans so I've stuck with it.

Of course, if you've got money coming out your ears, build everything! (except farms in places you don't want with an exploding population) Also, I HIGHLY recommend academies and other such buildings in any city that will have a long-term governor. Unlike MTW, you can get excellent leaders if they sit around and do nothing, as long as they are in a town with good 'schooling'.