The same problem here after an upgrade to Karmic (amd64).

I did some testing and came up with the following two workarounds:
1)Start the game emulation from the terminal using the "fceu" command.
2)  Disable Pulseaudio before starting "gfceu".

The 1st workaround bypasses the graphical front-end (gfceu) while the 2nd 
workaround ensures that the audio is not being passed to the pulseaudio daemon.

Checking the dependencies of the "gfceu" package i would guess that the problem 
lies somewhere in the combination of the "alsa-oss" package and pulseaudio.

Greetings René

P.s. For the sake of completeness i will list the steps to be taken for each 
work-around.

Work-around 1:
* Open a terminal (Applications -> Utilities -> Terminal)
* start "fceu" with the following command:
        fceu /path_to_emulator_rom/emulated_game.nes

Work-around 2:
* Open a terminal (Applications -> Utilities -> Terminal)
* Copy the "client.conf" file from "/etc/pulse/" to "~/.pulse/" using the 
  following command (this only needs to be done once):
        cp /etc/pulse/client.conf ~/.pulse/
* Edit the client.conf file in ~/.pulse/ 
        replace the line:       ; autospawn = yes
        with:                           autospawn = no
* Kill the pulseaudio deamon with the following command:
        pulseaudio -k
* Play the game using the graphical front-end (gfceu)
* After playing the game pulseaudio can again be allowed to autospawn by 
editing 
  the mentioned file above and inserting an ";" before autospawn = no.

-- 
games unplayable when audio is enabled, massive slowdown.
https://bugs.launchpad.net/bugs/424858
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