Heyho,
I am using the separation-of-variables method for quite a while now, but what was always bothering me a bit, is why is it possible to do those operations. I'll give a concrete example (source Wikipedia):
$$\frac{dy}{dx}=xy^2 + x \Rightarrow \frac{dy}{1+y^2} = x \:dx \Rightarrow \int{\frac{dy}{1+y^2}} = \int{x \:dx} \Rightarrow \cdots$$
and so on. My problem lies in step 2. Why can I just treat the differential operator like a variable?
Maybe the best way to see what's going on is to write it as an "almost separation of variables", where you separate the variables except that you keep the derivative intact: $$\frac{\mathrm dy}{\mathrm dx}=xy^2 + x \implies \frac{1}{1+y^2}\frac{\mathrm dy}{\mathrm dx} = x$$ This is clearly a valid transformation. And it is also valid to integrate both sides over the same variable: $$\frac{1}{1+y^2}\frac{\mathrm dy}{\mathrm dx} = x \implies \int \frac{1}{1+y^2}\frac{\mathrm dy}{\mathrm dx}\,\mathrm dx = \int x\,\mathrm dx$$ Now on the integral of the left hand side, you can do a variable substitution from $x$ to $y$. This gives $$\int \frac{1}{1+y^2}\frac{\mathrm dy}{\mathrm dx}\,\mathrm dx = \int \frac{1}{1+y^2}\,\mathrm dy$$ and therefore you get $$\int \frac{1}{1+y^2}\,\mathrm dy = \int x\,\mathrm dx$$ But that's exactly what you get by doing separation of variables the usual way.