There are lots of terrific graph theory books now, most of which have been mentioned by the other posters so far. I would particularly agree with the recommendation of West; one of the most complete and well-written texts there are.
But to me, the most comprehensive and advanced text on graph theory is Graph Theory And Applications by Johnathan Gross and Jay Yellen. Crystal clear, great problems and contains probably the best chapter on topological graph theory there is in any source by 2 experts in the field. It's pricey, but well worth it.
And of course, anything by Bollobas is beautiful. The problem with Bollobas, though, is that it treats graph theory as pure mathematics while the books by Gross/Yellen and West have numerous applications. Like linear algebra, the applications of graph theory are nearly as important as its underlying theory.
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