I recently upgraded my ubuntu 11.04 to 11.10 and then noticed that sound output started cracking when I played mp3 files or youtube videos.
The only solution at the moment is to reduce PCM value in alsamixer terminal window
Type alsamixed at terminal :
A window would come up with multiple vertical bars. 3rd one in them is PCM. Reduce it , this should remove the cracking sound problem. Or you can try reducing the sound in gnome-sound-applet
Some description of the bug :