White Balance/ Filters
The ability to set custom white balances largely makes color filters unnecessary.  The only thing they really (potentially) offer is better dynamic range.  With a white balance adjustment, it alters the processing of what the sensors pick up, but if there is a really bright orange area for example, it could overload those sensors and thus detail would be lost if the rest of the image was darker.

Using a filter would reduce the amount of light of that color reaching the sensor and could potentially keep more detail.  This probably isn't going to happen in the vast majority of cases, but it is one physical difference between the two processes.  For the most part, color filters are a hold over from film days when there wasn't electronic white balancing.