I haven't seen anything that lets you directly reprogram the stock ecu, But next gen has a fuel Tuner that you can hook to your lap top and use it to max out your fuel - air ratios over your power band. Same Idea as reprograming your ECU to do the same.
http://www.nxtgenmotorsports.com/HCart/ELC/ELCTR.htm
Thats the link to there order page. one is preprogramed to your MOds the other is not. both can be reprogramed in the future to keep up with your additional mods.
Powerchip Has a chip that replaces your ECU with a new one programed to give you better HP torque etc. Its a replacement, but not reprogamable by you. If you change your mods, you have to send it back to them to reprogram. Ther program is also based on what octane gas you run.
http://www.powerchipgroup.com/index.asp
Nex gens would be nice if you have access to a dyno machine and a laptop to really fine tune your car. Power chip is more of a one time fix that will give you most of the benifits with out the dyno work. I havn't heard anything but positive remarks about both of those two chips.