I always figured Pippin was crying because he realizes the kind of man he's sworn to serve, and fears that Gondor cannot hope to achieve victory under the rule of such a man. Also I'm sure he's quite lonely, with no one he really knows in the city except Gandalf (who's always calling him a 'Fool of a Took'), and separated from his best friend and all. Basically I'm willing to agree with pretty much everything that's been suggested so far here - the poor hobbit really has no reason not to be crying at this point in time.
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Above all shadows rides the Sun and Stars forever dwell:
I will not say the Day is done, nor bid the Stars farewell.
-- Samwise Gamgee
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