A very interesting kind of existence (though not uniqueness) proofs are proofs that use one of the various fixed point theorems and the tools from fixed point theory: The Schauder fixed point theorem can be used to prove Peano's existence theorem or simple existence theorems for boundary value problems. The theory of Brouwer-degree of certain mappings (not just between manifolds but also between banach spaces) can be used to prove several existence theorems, for example existence of periodic solutions for certain ODEs.
Granas / Dugundji - Fixed point theory is a very good (and very densely written) book about all kinds of fixed point theorems and one of the main application that frequently occurs throughout the book are existence theorems for differential equations.
Then there is the variational approach: Finding minima of functionals often is the same thing as finding solutions of PDEs (Euler-Lagrange-equations !). So very much of functional analysis can be applied to prove various existence theorems for PDEs. For example have a look at Guisti - Direct methods in the calculus of variations. Any book on the finite element method (Braess comes to mind, but I'm not sure at the moment if it is in english or in german... may be there are two versions?) will show you how Hilbert space methods can be applied to prove existence theorems.
The whole theory of distributions was invented for dealing with (linear) PDEs, their (weak) solutions and the regularity theory of these solutions. The Ehrenpreis-Malgrange-theorem is a very strong existence theorem that says that all linear PDEs with constant coefficient have distributional solutions. In Fact there exist (tempered) Green's functions for every such PDE.
And there is of course a more heavy machinery too: Morse theory and generalizations of it were used for (invented for?) the proof of the Arnol'd conjecture which also shows the existence of certain periodic solutions of differential equations.