Deciding on which equations to number I’m writing a master’s thesis in theoretical and mathematical physics, specifically in general relativity.
To better organize the thesis, I’m using the well-known division in works in mathematics to organize important results in lemmas, propositions, theorems and corollaries.
Outside those blocks there are also equations relating to the overall discussion connecting the results.

I’m quite unsure about the equation numbering. I see several options:


I number all equations.
I number only the important ones which I’ll need later.
I number just the equations on the discussions and not those inside the proofs of the lemmas, propositions, theorems, corollaries, etc.


What are the pros and cons of these approaches?
(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.