I have had a ton of luck with CareerBuilder. All the other ones--Monster and such--have been completely useless to me, but I've had several good opportunities via CB, even if I didn't wind up taking all of them.
I have also had good luck going to company websites directly.
And I too find that, if they're interested, you usually hear back pretty soon. If I hear, I hear within a week or less. If I don't hear within that week, I assume I'm out of the running (and prepare to be pleasantly surprised if I'm not).
As far as calling the potential employer, these are my thoughts. If you've just sent in your resume and haven't heard anything at all within a week or so, it's probably not worth it to call because you're probably not on their short list. Direct your time and energy to applying for other jobs. I wouldn't avoid calling because I'm worried about annoying the person. If they weren't going to hire me in the first place...nothing to lose in that respect. It's just a matter of spending my own limited time and energy wisely.
However, after they've contact edyou (for a phone interview or an in-person interview or whatever), I think it's perfectly OK to follow-up a few weeks later if you haven't heard anything. Just something like: "Wanted to let you know I'm still interested. Hoping to hear back from you soon." or whatever.
2b-ish--embracing my waves this summer
Aussie Catch the Wave condish, L'Oreal NutriGloss condish; Nexxus Designing Texxtur Cream, Rusk Radical Creme, Pantene Curl Defining Mousse, Paul Mitchell Sculpting Foam; coconut oil for DTs