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Mostly it depends on what you are measuring. Always there is compromises to make. You can not get 1Gsamples with S/N ratio of 100dB, and resolution of 24bits!
Please be more specific.
Simce
My idea is that you should use a mix of the three.
Analog prefilter is mandatory, and depends on the bandwidth of interest.
Software averaging is a good idea and I suggest to use it when possible. It gives good results since average noise is zero. Use it for example when you have to compare slow signals or to display measures. You cannot use it when you need fast sampling of fast signals.
If you use your converted signals for digital control loops, probably you do not need averaging, since the filtering effect is probably included in the digital algorithm and depends on the bandwidth of the loop.
That depends what you will measure and with all presicion wants to measure it, however an integrated ADC of 10bits to my personally me to resolved all my problems, notice the Motorola HC8MR32.
A good Timer is very useful for measures of AC.
It specifies what you want to make better and I help you better.
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