Short bio: Computer Scientist, FOSS supporter (read more)
Tux Machines (TM)-specific
These days the GUI mixers KMix and GNOME Sound Preferences display PulseAudio devices and streams rather than ALSA mixer channels.
KMix 3.8 in KDE 4.6.1 does not provide separate speaker and headphone channels. You can alter the headphone and speaker volume by using PulseAudio Volume Control instead (see the picture below), but people are not as familiar with the PulseAudio GUI, and it is yet another step to perform.
If you are like me, you probably end up using KMix (or GNOME Sound Preferences) but also launch ALSA Mixer in a Konsole/Terminal for fine-grained control of the underlying ALSA channels.