Do games benefit more from having brute speed or having more than 2 cores

The answer is going to vary with every game, no two games are identical.
As a general rule (and there are certainly a number of exceptions) games aren't very well threaded, they'll generally use two cores fully and may touch upon using a third core but not enough to be particularly meaningful. Even if the game doesn't use more then two cores, it's not entirely wasted as any background tasks can and will happily run on those extra cores.

That said, things are slowly improving over time and we're ever so slowly starting to see games that see a meaningful benefit from more then two cores.
With respect to the games you've mentioned, most of them I don't know but those I do:
Portal- Two cores, any more won't yield any benefit.
Fallout 3-Two cores is just fine.
GTA 4-Feed it as many cores as you can. You'll definitely lose out with two cores.

Bottlenecks depend on the specific game and resolution. Assuming you're running at 1920x1080 or above then you're likely to be GPU limited in most cases even with a relatively weak processor. If you're running at lower resolutions though you're likely to start running into processor bottlenecks. If you're at 1366x768 or something then a GTX 560 Ti is ridiculous overkill.
This will vary depending on the game though.

6 cores is a complete waste for games, even the most highly threaded games aren't seeing much beyond 4 cores. I wouldn't count on this changing anytime remotely soon, it's incredibly difficult to find enough non dependent work to push across 6 thread, and frankly even if it wasn't that's a ton of extra complexity the developers are going to have to deal with and for most it's not going to be worth that extra time and expense for what's likely to be of very dubious benefit.

As for a graphics card recommendation, without knowing your budget it's hard to make a solid recommendation. Whether you're concerned with pushing AA, must have the highest detail settings in-game or willing to compromise a little there would be nice to know as well. What resolution you're generally playing on makes a huge difference as well.

My roommate runs an e8400. Just last week he decided he wanted more power as he bought into tera and diablo 3. He was previously running a HD4850 1GB.

He upgraded to a 2GB GTX560Ti, and effectively doubled his framerates in all games. Went from around 45 FPS to 60+ in tera maxed. D3 he laughs at, and tribes ascend he gets well over 100 fps now.

I'd say its a damn fine choice of a card to go to on that particular chip. Anything more, and yes you're beginning to worry about your FSB being the bottleneck. But that card, fucking golden and i want one.