Just as Stereo and Home Theater are very different there isn't a single answer. The only constant is that every room has its unique issues and peoples taste differ widely. For some Room Correction and or Equalization can be a good place to begin their manual adjustments.
A flat response is what a reviewer might be looking for when assessing the performance of a speaker. While certain frequency adjustments might be to ones taste, generally it has a tendency to make well designed speakers sound like compressed AM radio. In the low frequencies cutting frequency spikes can be very beneficial.
Having a sound reach your ear when the sound engineer designed it to maybe the more important goal of Room Correction as it pertains to Home Theater. If you have the room, placing identical speakers at the same distance and height from the listening position with the EQ off will give you a new found sonic base line for surround sound.
The typical issue with frequency equalization with Stereo is usually the boosting of mid to low bass, hence the Bass knob and the Loudness button on early receivers.
There is a small but growing number of audio systems such as Kii Audio that address room issues using another method. Voxativ's Hagen Absolut system is yet another interesting product. Both were quite impressive under show conditions. For me they imposed a quality that left me undecided.
