Deciding on which equations to number
(Maths/Engineering Copy Editor speaking.) Well, first, I advocate against these two solutions (see below for some reasoning):


Number all displayed equations.
Number only referenced equations.


So, the solution lies somewhere in between. The basic idea is that you do number:


All referenced equations (obviously).
All important equations. To measure this, I would say that an equation is important if the reason why you made it a displayed equation is to emphasize it.
Unreferenced equations "parallel" to a referenced ones. Imagine you have two similar equations in similar contexts in your work; then you should either number both or none.
Equations you "feel" (whatever it means) someone else might want to reference.


What you in general do not number:


Equations put on display for that they are too large.
Intermediate steps of computations.
Equations in abstracts.
You number a multiline equation only with one number.


Hope this helps. Almost-final words: Use your common sense. Final words: Be self-consistent.



Why I don't like all displays numbered:


It clutters the page if there are many equations. You also might number things that are basically one equation (think LaTeX's \intertext).
The numbering ceases to function as an emphasis.
If the equations are long or the columns narrow, it can eat up precious space.


Why I don't like only referenced equations numbered:


You don't allow anything else referenced than what you yourself decided to reference.