44.1, 48kHz those are the limits of the mp3 format.... more important is the bit rate you compress at, best results will be obtained by using 256 or 320 kpbs, do not use variable bit rate, do use Best Encoding and Filter frequencies below 10hz.
Depending on the type of music there -may- be some benefit using 96khz. Such as using all Soft-synths with a lot of effects. If you have a mixture of recorded audio, vocals, guitar, percussion...96kHz is overkill in my opinion and stresses your computer needlessly. You need to have pristine recording conditions/microphones/monitoring system/room to take advantage (if any) of 96. I would start at 48kHz. Again, it depends on the music.
Last... a professional method of getting it done, (whether you start at 96, 48 or 44.1), Always use 24-bit.
1. (Important) Get your mix the way you want it! Do not be concerned with overall volume.
2. Bounce the mix to high quality a stereo 24-bit AIFF or WAVE file at the sample rate you started with.
3. In a new project import the mix This will be the file you Master.
4. Tweak the stereo wave/aiff file to your liking using plugins on the master bus, compression/limiting/eq...etc.
5. Bounce the Mastered file to the same type of high quality file with a new name, at the same time you can bounce to an mp3 file.
Yes, it's time consuming, but it will give you the most options... for CD the high quality master can be converted to 44.1, using a CD mastering program which usually handles the conversion automatically, or you can do it in Logic.
