Let's consider the simple differential equation:
$$\frac{\partial^2 u}{\partial x^2} + \frac{\partial^2 u}{\partial y^2} = 0$$
And let's assume we have some regular homogeneous boundary conditions like:
$$ u(a, y) = 0$$ $$ u(L, y) = 0$$ $$ u'(x, y) = 0$$
(I just made these up at the top of my head so feel free to improvise if they don't work with what you want to say.)
My question is: What is the intuition/motivation needed in taking a product solution of the form: $$\Psi = X(x)Y(y)$$ From what I understand, we also assume that the BCs apply to $\Psi$ too.
From what I've been told, there is no proof of this, it's just a reasonable trial that seems to work well in a lot of cases.
It is probably impossible to say for sure what brought Bernoulli and slightly later (thans @mkl314) Lagrange to consider a product of two functions as a solution of the wave equations. However, a good guess would be: the knowledge that the wave equation describes, well, waves. D'Alambert actually already written down his formula that provides a direct interpretation in terms of traveling waves, however, it was well known to all the great names I wrote above, that, given some conditions at the boundaries, what is observed in an experiment is the standing waves (Bernoulli in his paper from 1753 gives drawings of his father, who did a lot of experiments considering waves). And it also was well known that the simplest analytical representation of the standing waves is $$ A(t)\cos (\omega x+\phi), $$ hence a guess to look for a solution in the form $$ T(t)X(x). $$ And, of course, Fourier came later to claim that any function can be represented by its Fourier series to provide a (nonrigorous at the time) justification of the method for the linear equations for which the superposition principle holds.
Added: See here Bernoulli's paper with obvious "Fourier series" and especially with figures on standing waves.