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There are those who consider that papers look untidy with numbers on every equation; there is also a school of thought that claims that there should be numbers everywhere, in case some reader wants to make reference an equation to which the author made no cross-reference.

If you hold to the “only cross-referenced” school of thought, you can (using the \nonumber command on the relevant equations, or by using the AMSLaTeX unnumbered environments such as equation*) mark those of your equations to which you make no reference. In a long or complex paper, this procedure could well become deeply tedious.

Fortunately, help is at hand: the mh bundle’s mathtools package offers a ‘showonlyrefs’ switch through its \mathtoolsset command; when that’s in operation, only those equations to which you make reference will be numbered in the final output. See the package’s documentation for details of how to make references when the switch is in effect.