I recently upgraded my desktop to a 3.0gig Intel Dual Core. I decided against the quad because the same money would buy a slower clock speed. The way I see it, the extra cores are only good if you have applications that are designed to use them. Windows will assign each application to only one core, unless the application knows how to deal with multiple cores. I doubt any of the programs you listed can handle multiple cores.

Yes, if you are using multiple applications at once, you might get some boost from a quad core. However, I realized that mostly the extra applications are idling and don't take much processing power. I decided that maximum performance per core was more important to me, at least with the current generation of software.

For the multiple applications you listed as running at once, I think it's more important to max out the memory than to go to a quad core system. Put 4gb ram in, and make sure that it's the maximum speed your motherboard can take. Also, many motherboards access ram faster if you have a pair of memory sticks in the right slots. If you are buying a pre-made system, you won't have control over that.

A 350 gb hard drive is probably fine, although a Seagate 1Tb drive is now under 150 bucks across the counter.

One more thing, make sure the video card you choose can handle a pair of monitors (usually one digital port and one analog port). You might not need it now, but in the future, it will be as simple as plugging in the second monitor. With all those applications running, you'll get more work done with two monitors.