This may not be formal enough for an answer, but it doesn't seem like you're looking for a purely formal answer.
I would say that $X = Y$ is meant to express that in certain contexts (sometimes explicit and sometimes less explicit), anything that is sufficiently involved in $X$ by some witness can be turned into something sufficiently involved in $Y$ by an analogous witness and vice versa.
For example, in a commutative place $x + y = y + x$, and $2 + 3$ is sufficiently invovled in $x + y$ by the substitution $x \mapsto 2$, $y \mapsto 3$, so we can replace $2 + 3$ by $3 + 2$, which is sufficiently involved in $y + x$ by the same substitution. (Of course, I had to use a notion of sameness to explain a notion of equality...)
Or, if $X$ and $Y$ are isomorphic by some isomorphism $f : X \cong Y : f^{-1}$, then any 'element' $a : A \rightarrow X$ can be turned into an element $f \circ a : A \rightarrow Y$ ('witnessed' by $f$), and vice versa, and any element $b : Y \rightarrow B$ depending on $Y$ can be turned into a element $b \circ f : X \rightarrow B$ depending on $X$. (Note that it might be the case that $X$ and $Y$ are very different mathematical objects --- the set of primes and the set of integers, isomorphic as sets, for example --- but may nevertheless be usefully considered 'equal' in some context.)
Clearly anything sufficiently involved in $X$ can be turned into itself by doing nothing, so this 'relation' is reflexive. And so long as we remain consistent about our criteria for being 'sufficiently involved' and our means of turning witnesses for one involvement into another, this relation will be transitive. Of course, 'consistent' here probably invokes a notion of sameness, so I haven't defined equality so much as used it. I'm not sure there's much of a difference.
Symmetry is also a subtle thing because it constrains the ways we can turn things which are involved in $X$ to things that are involved in $Y$. If instead of an isomorphism between $X$ and $Y$ I just had two functions $f$ and $g$ going opposite ways, then I could still turn things involved in $X$ into things involved in $Y$ and vice versa, but I would not be guaranteed to get the same (there it is again!) thing when I did these processes one after another. Where in a general case I might not have $g \circ f \circ a = a$ (where $=$ here is a prior notion of sameness), I will always have $f^{-1} \circ f \circ a = a$. Careful relaxation of these constraints gives us notions of equivalence and adjunction which can be quite expressive (e.g. models and theories may be interchanged, but at a cost).
About that pesky recurrence of synonyms (same, similar, analogous) when trying to define equality: We could say that "Equality is the smallest equivalence relation on a set", or "Equality is the graph of the identity function", both of which are true (and give the same relation) but of course both depend on a prior notion of sameness. The second wears this prior notion on its sleeve in the definition of the identity function $x \mapsto x$. The first seems like it might not invoke any prior notion at all, except that without a prior notion of sameness it isn't clear that there is any smallest equivalence relation on a set. Whatever the smallest equivalence relation might be, it will be nothing more (and, of course, nothing less) than whatever we thought it would be.
Usually we take this to be some kind of syntactic equality, or something of similar context independence (definitional $:=$, as dbanet says above, or judgemental $\equiv$). But even this is not free from issue because sometimes people have terrible handwriting, or are making notes and changed their use of a symbol halfway through the page, or whatever other shenanigans the world can throw in the way of honest mathematics.
Ultimately, equality is done. We make things equal by treating them as such, whether it be two differently scrawled $x$s on a blackboard or two quantities coming from widely different fields. Generally, however, we don't have the kind of freedom that statement might suggest. We try not to wreck our so-far-consistent edifices with indiscriminate equalities. And, more importantly, we are often led, coaxed, or even commanded by the things we talk about to treat apparently different things as equal. We can't really do mathematics without doing equality, and how we do mathematics tells us how to do equality.
On a less bloviating note, I think what you may need about equality is a notion of context dependence. If we just take the equality relation on a set we know nothing about and are doing nothing in particular with, then the equivalence classes can only be singletons because that kind of equality is presumed no matter what. But if we are working not just with any set but with the numbers, and we're adding them, then $1 + 1 = 2$. Or, perhaps a bit more precisely, if we're working with formal sums of numbers (call this set $S$), then the equivalence classes will be quite large. But $S/\sim$ will be the numbers, and again equality here will be singletons. So it depends where we are and what we're doing.