Besides, many good jobs are not even listed on the big job boards.
Recruiters, guys. Do you know there is a whole class of people that will work full-time to bring you whatever jobs you want? Why am I the only one mentioning them in this thread?
Because most recruiters are ignorant incompetents, or at least most of the interactions that potential recruitess have are with ignorant incompetents. If you want a longer, more involved version of this look at Peroni's comment history, (formerly KoZeN).
I am mostly curious about companies specific to the bay area but a larger scope would certainly be welcome.
If the Internet is just "Facebook" + "Google" to you then, sure you're missing out but by just posting to HN I'm guessing that isn't your world.
If you mean super early startups (and be mindful that there are plenty of reasons not to be the first employee at an unfunded/newly funded startup) then Angel List is probably the "magic resource" you are aspiring for.
Then you can do some research on company x and try to get in touch with someone there.