http://www.ctan.org/tex-archive/macros/latex/contrib/hyperref/ has this note copied below:
amsmath
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The environmentsequationandeqnarrayare not supported too well. For example, there might be spacing problems (eqnarrayisn't recommended anyway, see CTAN:info/l2tabu/, the situation forequationis unclear, because nobody is interested in investigating). Consider using the environments that packageamsmathprovide, e.g.gatherforequation. The environmentequationcan even redefined to use gather:\usepackage{amsmath} \let\equation\gather \let\endequation\endgather`
However, gather and equation environment have the spacing difference as in the answer by Will in align vs equation. Thus my question:
In a document using both hyperref and amsmath, what is the best replacement for equation?