This question has been asked before but in relation to performance. The SO answers omit issue of implementing on IE.
I accept that CSS3 Transitions are faster than jQuery animations.
However I note that CSS3 runs into problems with IE 6-8 and would therefore require the use of a plugin like ie9.js or select[ivizer]. Both of which have varying write ups both on SO and elsewhere.
Therefore I would like clarification here. It is my understanding that jQuery animate will normalise across browsers and versions thereof.
Thus even looking back to ie-8 is best advice to use jQuery regardless of any hit in terms of speed?
This is somewhat a matter of personal opinion and personal needs,
My recommendation is to stick with jQuery if cross browser support is a concern, seeing as CSS3 is still changing rapidly across browsers. Although CSS3 does prove faster at various benchmarks.
Alternatively, you can use specialized plugins that use CSS3 transitions and fallback to animate when an unsupported property is found, a good one would be jQuery Transit, although it does not have the complete solution for all needs.