Upsampling - where it's actually done - is like digital zoom. The inbetween stuff is interpolated and doesn't really make much difference, although some people like to think it does. If it's audio, keep it 16-bit/44.1khz.
Yeah, I recommend keeping it in the original bitrate and sampling rate. The exceptions are with MP3's (use highest bitrate that your soundcard or source can actually handle but keep the sampling rate the same as the original) and if your soundcard does internal resampling. A lot of soundcards will always resample the audio (usually to 48 Khz) internally when they apply any kind of processing (3D effects, EAX, or just for shits and giggles (Thanks Creative)). For these cases, you may want to set it to 48 KHz just so you do not unnecessarily make the soundcard upsample to 48 KHz and then downsample back to 44.1 KHz for analog or digital output (your speakers don't care). In addition, some people feel that some software resamplers (Like PPHs for Foobar) do a better job than the hardware so they upsample the stream to 48 KHz instead of letting the soundcard do it.
But this has been improved with Vista and Windows 7 with the incorporation of WASAPI (earlier there was ASIO too but that was always a bit dodgy if your sound device did not have ASIO drivers). WASAPI can allow you to directly output the sound to the output device and avoid some of the Windows software layers. I think this is mostly helpful for digital outputs since it keeps the digital feed unmolested but if you are using analog outs then it probably still goes through the soundcard's processors.
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