The "best" channel frequency to use is one that other networks and wireless and devices are not using.
For most users, the "Automatic" channel setting works well, since the AirPort will automatically scan to select the "best" channel to use.
If you are asking about whether to use the 2.4 GHz or 5 GHz band of frequencies.....most wireless networks (and cordless phones) use the 2.4 GHz band, so there are far more chances to pick up interference on that band.
If your devices are all capable of using 5 GHz, you will likely have the best results using that band. The downside to 5 GHz is that these frequencies are not as strong as 2.4 GHz signals, to 5 GHz signals will be absorbed more quickly by any obstructions like walls or ceilings.