This is a complete stab in the dark, but it could be that your sound is working but that one application is holding your sound-card open and others can't access it. One solution to this problem is to install a software mixer such as alsa-oss.
In case something is holding your sound card open, you can run this to find out what it is:
lsof /dev/dsp* /dev/audio*
There are other options, such as having multiple sound cards/chipsets detected (and the wrong one being used), or having an amplifier setting set to mute, but I would expect those to show up in the configuration tools.