Are you talking about a 3.5mm audio output or headphone jack?
The two are completely different. The optical (or coax SPDIF) output is the raw digital signal as encoded in the digital file (MP3, MP4, etc.) or DVD/Blu-Ray. This digital signal gets decoded and converted to an audio signal by a digital to audio converter. The 3.5 mm output is a fully decoded analog audio signal. It's already been decoded and converted by the D/A and processors on the sound card or sound chip. Alternatively, you can send the original digital signal from an optical output to an external decoder and D/A converter (such as a home theater receiver).
The original digital signal can send stereo and Dolby Digital encoded surround data. The menus on the DVD/Bluray...