I'm looking into making a build something like Logan's Honey Badger and I'm wondering if the added airflow from the mesh on the front of the Black Prodigy actually effects anything. I'm fine with black but if there isn't a difference I'd probably rather go with the Red or Orange (just for the sake of making an obscenly obnoxious machine to use at lan parties and such)
Mesh will be better for airflow since it will obviously allow more air to come in than the standard grating around the edges. That said, if you really want to have either a red or orange case, BitFenix stocks several variations of the mesh front panel that you can buy separately. All of them use a black mesh with a varying color trim though. But if you don't mind the constrast, you could look into that. They're on BitFenix's website under Products > Accessories > Prodigy Custom Front Panels, but their store seems to be down for the moment.
It really depends on how hot you expect your system to get. If you plan on overclocking, I would say getting either the black model or one of the colored models with a separate front panel would be your best bet. If your running everything at stock or with a modest overclock and your using decent coolers on your CPU and graphics card, then you should be fine.