non-profit-organisations have their H1 excluded from 65K limits of H1 approved each year. So posibly, you can not transfer...

 so if i get a new job at profit company, can i transfer from my non-profit (if there is stil quota left) or does my new employer need to reapply

I would say it needs to be reapplied.

@ans thanks for the answer, it may not be transferred but i can still apply for a new H1B as only 17k out of 65,000 H1B for fiscal year 2012 has been filed.  but can i start working for my new employer immediately? what about if it is approved before october 1,  (the quota system will allow us to start working only after october 1)  .  it does  not make sense that  a person whose case is pending for H1B approval is in a better shape (continue working for new employer) than a person whose H1B is already approved before october 1 (has to stop working for new employer as soon as it is approved since the quota system is considered to start only after oct. 1) 

@the_hareeb  we can definitely go ahead and work for the new employer (for-profit company) in future but the only confusing part is whether it should be filed as a new H1B or a transfer of H1B.

@anon  i also thought it needs to  be reapplied going into a quota system from a cap-exempt, but talking to my possible  new employer's lawyer yesterday said, it can be transferred. i told him i couldn't find anywhere which says that i can transfer my H1B from non-profit org. to for-profit company. but he was firm with his words and i couldn't satisfy him in any ways due to lack of source. i thought maybe he knows better than me and he should but i am little worried now if during a transfer process it is rejected (hope not) by USCIS saying it cannot be transferred and i will have already left my old job and i cannot join the new one. this might jeopardize my status. so i was looking for someone who had similar experience.

forgot to mention after talking to the lawyer, i did some more research and found the second source (link  in my original post) which clearly says:

H-1b cap-exempt moving to an cap-subject employer:  if the hospital is hiring an individual who has been working on an H-1b through a cap exempt employer, the non-exempt hospital  needs to wait until April 1 to file the H-1b transfer.   The individual can work between the April 1^st filing and October 1^st based upon H-1b portability if the underlying LCA and H-1b petition for the cap-exempt employer will carry through until October 1, 2011.


so now i am really confused what to do.......

 If your H1 was transferable,  you do not need to wait until April 1st. Once your new employer files LCA for new job, you should be ready to go. It takes max. a week for the LCA to get approved. 

But since yours is different story, it's a bit confusing. Talk to your new employer ..