One of the biggest problems in mathematical physics is actually to understand the link between Hamiltonian/Lagrangian mechanics and functional analysis.  This is because classical mechanics is formulated in the former setting while quantum mechanics is formulated in the functional analysis setting.  The act of going from classical mechanics to quantum mechanics is called quantization and basically consists of assigning functional analytic operators to classical observables, in a way that respects the Poisson and Lie brackets.  For example in classical quantization we assign position to the operator of multiplication by x and we assign to momentum the operator $-i\frac{d}{dx}$.  Both of these act on (a dense subset of) the space $L^2(\mathbb R)$, which is taken to be the space of wave functions in one dimension.  You may want to take a look at the orbit method, which is the mathematics involved in a quantization scheme called geometric quantization.

Some relevant MO discussion about this are:

http://mathoverflow.net/questions/6200/what-is-to-quantize-something

http://mathoverflow.net/questions/8606/what-does-quantization-is-not-a-functor-really-mean