that is when using high shutter speed with flash, such as 1/160, 1/200

You can use a SB900 to become the commander, or a SU800 for it. But your pop up cannot do commander mode like D90 and above.

D3000 and D5000 does not hav the build in flash commander function, means ur build in flash cannot Trigger other flash wireless which is not mounted on the hot shoe(mounted on the flash stand away from camera body)! However if U wan to do this, u can use SB800 or SB900 which has the commander function(mount them on your camera body and trigger other flash wireless), or change ur camera body =)
Hope I made this right....

Info courtesy of General_Nic

Di622 with latest firmware can be radio triggered, using radio waves from body built-in commander(D90 n above), or SB900 or SU800. Di866 should b able to do both since the younger brother Di622 can do it!!

specs list:
Di622 - optical n radio trigger
SB600 - radio trigger only
SB900 - optical n radio trigger

(optical trigger means triggered by pop up flash, when the pop up flash fires, the other flash <ie. Di622 and SB900> sensor detects it and instantly fires together as well) this happens instantly. So u will juz see both flash firing together

there r many good flash out there, it all depends on your budget
most common r:
Nikon SB600 - rm800
Nikon SB900 - rm1600
Nikon SB800 - rm1100(2nd hand)
Nissin Di622 - rm450
Nissin Di866 - rm900

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Added on April 30, 2010, 12:02 pm

D3 shud have, cos CLS is a special feature of Nikon
Canon similar feature only their top of the line 1D/1Ds have it, now 7D has it
its jz not logic for flagship model to not have
jz my theory, sory if im mistaken 

about pop up flash trigger, im not sure
jz heard frm other ppl say in order to eliminate the pop up flash harsh light during close up shot
they block it with a card

Suit. Im using now