I upgraded to Ubuntu 9.10 in early December, but yesterday was the first time I tried to use headphones since then.
It turns out that plugging headphones into the headphones socket doesn’t automatically mute the speakers anymore.
Here’s a fix.
Open a terminal (Alt+F2 > gnome-terminal)
Use the arrow keys (left/right) to highlight Headphon
This should fix it. You can now hit Esc to exit and exit the terminal.