I've recently acquired an E-MU 0404 USB, so perhaps my experience with it can help you.
After some struggle, it seems capable of playing back both 44100Hz and 48000Hz (and, probably - but I've not checked - various frequencies up to 192kHz...)
GStreamer's capable of doing sample rate conversion, but it's probably not the correct place to configure this. As you've doubtless noticed, how one would configure it is incredibly obfuscated and would likely involve gconf. However, there's a number of other locations that should work. I've listed them in descending order of preference.
The trick with these devices appears to be to set the 'Clock Rate' slider in the the mixer (the terminal based alsamixer should just show it, I think others require you to unhide the slider). Setting it to 0 gives 44100Hz, 1 gives 48000Hz, and so forth. Irritating - but workable.
Note; If you want to use the SPDIF output, you need to configure your media player to output from device 1. if anyone's trying to get passthrough (AC3/DTS), this won't work, unless your sample rate is set correctly (usually, the 48000kHz aka '1' setting).
At this point it should be working, below talks about how to do things without fiddling with that slider:
If you really want to do sample rate conversion, you should be able to get the desired effect by creating the appropriate ~/.asoundrc (this assumes that the E-MU is the second sound device - you can check with aplay -l). The following is untested as I've not got analogue cables handy for mine:
Configuring by ALSA should have got things working, however, if you'd prefer to configure it via PulseAudio, edit /etc/pulse/daemon.conf
and make sure the default-sample-rate line reads (ensure it's not commented out with a ';' and the number is correct):
default-sample-rate = 48000
(from https://wiki.archlinux.org/index.php/PulseAudio#Choppy.2C_overdriven_sound )