I have a strange problem on my 12.04 LTS machine: Sound works OK in wine (using spotify for instance), but none of the native linux apps are able to produce any sound. I tested rythmbox and VLC player, and they both show the same behaviour; they seem to play ok (progress bar moving etc) but no sound can be heard anywhere.
First, check in "Sound Settings" that correct outputs are selected, sound cards are properly configured, and that applications playing sound are listed in the "Applications" tab. If you think everything there is correct, install PulseAudio Volume Control.
Check that the correct device is selected as "Fallback" (in the "Output devices" tab), and then that applications currently playing sound are playing it on the correct sound card (Note: If something has HDMI output, it's very likely to show up as a sound card). Finally, check if the applications themselves are not muted in PulseAudio Volume Control.