I think there is something in numbering also equations which you do not refer to: if it is a publication to be used by other, they might want to cite your work with some specific reference to a particular equation. However, that might clutter your document quite a bit and produces large numbers ;) So my private convention is to number all equation except those which are inside a proof-environment. I guess this is quite fair, because if someone else wants to make reference, she can do so by referring to the lemma/theorem/etc which, of course, has a number.
Inside proofs, one has of course also the need to make references to earlier steps of the proof. But here I use \tag{$\ast$} instead of a number, which I understand to be a local numbering valid only inside the proof - there might by various equations inside proofs having the same symbol ($\ast$) but they are referred to only within the same proof. It also allows you to use nicer symbols for "local" equations like \smiley etc.