graph eigenspaces (with default settings, maybe they can be tweaked?) are 
quite adequate for up to 25-30 vertices, then it get very slow, indeed...

For the kind of computations you have in mind, I prefer using cvxopt (a Sage 
package); although it's primarily 
for optimization, it has a nice sparse matrices support, and nice LAPACK 
interface:
http://abel.ee.ucla.edu/cvxopt/userguide/index.html

its interface to Sage is quite rudimentary, but still...

Dima

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