Updates:
        Status: Fixed

Comment #5 on issue 1840 by [email protected]: atoms is non-greedy
http://code.google.com/p/sympy/issues/detail?id=1840

Oh, right. I didn't notice that the behaviour of.atoms() had changed.
I bisected it to the fix for issue 2007 (which was actually a duplicate of this):

commit 2a366eaf6b1b5e686c80a365461d4ba4b00b5cba
Author: Chris Smith <[email protected]>
Date:   Tue Aug 3 09:56:44 2010 +0545

    2007: atoms-recurses for non-atoms

    As long as expr is not an Atom, the search for "atoms" should continue
    so that exp(exp(x)).atoms(exp) should give exp(exp(x)) and exp(x) and
    (1+x*(2+y)+exp(3+x)).atoms(Add) should give the orignal expression,
    2+y and 3+x.



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