I've tried to work in different sample rates and have experienced the following. (I've got nebula libraries in different sample rates)
When working in 44k/48k it's easy to let nebula downsample from 96k. I can even set the RATE CNV to 50ms when working in 48k.
When working in 88k/96k nebula needs higher RATE CNV (3000+) to upsample libraries in 44k (and sometimes my nebula froze even though my pc wasn't overloaded).
The problem I have working in lower rates is that one of my vst drum samplers (Poise) is aliasing (creating it's own ugly distortion) a lot (working in 44k).
I've learned that many software work in higher internal sample rates to avoid this (one guitar amp simulator I have works in 172k). Especially software synths sounds a lot better working in higher rates even though the final mixdown is in 44k.
My conclusion is:
1) Work in lower sample rates then if you are lucky all your software synths/samplers/filters etc are programmed to oversample internally and you continue happy with more free harddisk space. *) The negative part is that this is more CPU consuming
2) Work in higher sample rates then you need to worry less about the softwares internal sample rates and you continue happy with more CPU power available. *) The negative part is the harddisk space *) Less CPU power used in the software plugins as the audio interface works harder (and the operating system), but in the end less CPU is used? (am I correct here?)
3) Working in higher sample rates is not about working in higher frequencies you're not even able to here anyway, but it's about that some software need this if they can't handle it internally.
3rd Party Library developers... Please sample in 96k or at least use a good sample rate converter to upsample and create a 96k version (even r8brain free is one of the best according to this site: http://src.infinitewave.ca/). If you have only sampled in 44k you may use one of the conversion tools to create a 96k library without spending to much time on this, correct?
(update about the sample rate tools: SOX 14.2.0 VHQ is one of the top converters and better than r8brain)