Yes, you are allowed to take extra lithium laptop batteries in your carry-on, but you may not check most extra lithium batteries (that are not installed in a cell phone, camera, PDA, computer, etc. - which you shouldn't check anyways).

For the definitive word, see here:

http://safetravel.dot.gov/whats_new_batteries.html

Note that this rule went into effect in the U.S. on Jan 1, 2008, so technically, the past experiences related above are not relevant, although they are also not in conflict with the new rule.