According to wikipedia,
For Konami,
Konami has two major studios, both in Tokyo. Konami Computer Entertainment Tokyo has Pro Evo, Castlevania and DDR in it's umbrella, and Konami Computer Entertainment Japan has MGS.
For Capcom,
They appear to have one main studio, however I'm not sure what all is outsourced. SF4, for one, is developed by Dimps. But right now, they should be mentioned for Monster Hunter Freedom.
For Square Enix,
I think you'd just want to list Square. Enix as a studio isn't really powerful anymore, and it doesn't look like their smaller studio has been absorbed into Square's main studio.
"[Our former customers] are unable to find software which they WANT to play."
"The way to solve this problem lies in how to communicate what kind of games [they CAN play]."
Satoru Iwata, Nintendo President. Only slightly paraphrased.
