Management. This is the one issue not really covered in the FAQ at this point so I'm going to try to lay out a basic framework of ideas, management options, and some of the goods and bads.
First of all, there basically two different types of fuel management available for our Hondas: Standalone and Piggyback.
Piggyback - A "piggyback" is a tuning system that works by manipulating sensor signals too and from the factory ECU. These systems are typically less expensive then the standalone systems, but do not control fuel and timing as well and therefore are not as safe and reliable to run. This is because a piggyback system is still relying on the stock ecu and its fuel and timing maps as a baseline. Though these maps are great for controlling the car without boost, they are not prepared for the introduction of more air into the motor. In fact, if your stock ecu reads positive pressure, it goes into limp mode. Stock timing maps are very aggressive especially in part throttle driving and since the piggyback systems are bound to the stock ecu you end up running considerably more timing then you normally would want with boost. This can lead to our evil friend we are trying to get rid of, detonation.
Probably the most common piggyback system is probably the Apexi AFC unit. This has been in the honda boost scene for quite some time now. Some people run it with an FMU and a check valve system to prevent the ecu from seeing boost while others run "the hack" which hides the boost from the ecu by using very negative settings. The afc is relatively easy to install and pretty easy to use. See above for downsides to the piggyback systems.
Other common piggybacks include the greddy blue box, the smc, and the greddy e-manage. The blue box used to come with the greddy turbo kits but has been replaced with a pre-programmed emanage system. The emanage is very similar to the afc in its tuning abilities while the smc unit uses knobs to tune ranges of fuel and the blue box is untunable.
Standalone - a tuning system that allows full control of both fuel and timing. They will allow you to more finely tune both of these to net the most power as well as making the vehicle much more reliable. They can read positive intake pressure (piggybacks can't) and can even use upgraded map sensors such as the 3bar (can read up to about 30psi of boost vs the 11psi of the stock sensor). There are many options in this area, so I'm just going to really get into the few that seem to be the most common and just generalize about the others.
Ok, first up is the Hondata unit. Hondata combines an obd1 ecu with their chip/box and software. This combination of designs creates a great system. Because it is based on a honda ecu, it typically has fewer quirks when it comes to making the car run smoothly and cleanly right out of the box. They offer two setups right now called the s100 and the s200. The s100 is a more basic unit that is designed to be tuned by someone else. It doesn't have some of the capabilities of the s200 such as datalogging, launch control, and full throttle shift. Most people will never use these options if the system is tuned by someone else anyways, but on to the s200. The s200 has a little blue box that sits outside of the ecu that contains ports to plug in a laptop for datalogging as well as the inputs for a clutch switch to take advantage of the extra features. To run Hondata, you must have an obd1 ecu (p28 is preferred) and have it socketed to accept programmed chips. You will also need an adapter harness to convert from obd2 to obd1 or you have the option of buying a presocketed p28 ecu from hondata with the obd2 connectors right on the box (very pimp). The advantages of the hondata are basically that its a tried and true solution from a company thats been around for a while in the honda business. There are many tuners who are familiar with its software and its software is very full featured (Real time tuning, two completely separate fuel maps for the high and low cams, etc). It has the same features as much more expensive units with less cost. On to the next option!