Do you intend to measure these capacitors in circuit? I mean without desoldering them? If so accuracy is not an issue, because you can't accurately measure a capacitor in circuit without considering the bits connected to it. In fact, I would say 9.5 or 9.9 times out of ten you cannot measure a capacitor in circuit at all.
The vast majority of capacitors on a motherboard are used for local power supply decoupling, which is to say they act as little batteries which are physically close to a fast chip, providing it with power until the main power from the power supply "gets there". Which is to say, the vast majority of the capacitors on a motherboard are connected together in parallel. There's no way of measuring one of these thousands of capacitors connected in parallel without removing it from the circuit.
That said, it seems to me that the vast majority of capacitor failures on motherboards are not with the little SMD decoupling capacitors, but rather with the bulk electrolytics. And the way those tend to fail doesn't really show up very well on a capacitance measurement, but rather an ESR measurement.
One thing to look out for with multimeter capacitances ranges is that they're often very limited. I find the capacitances I'm most interested in measuring is frequently outside the range of my multimeters.
Let me know if I'm on the wrong track here and you're already past this stuff.