I'm currently doing my second Masters here in US. I've already used my OPT after my MS in Computer science in 2008. I was also in H1B in 2009. Now, I'm back in F1 status (doing MBA) and working in CPT for a different company. Can I apply for the OPT again? what will be my process for the H1B if I've to apply for it? Do I again have to go through the same quota system? any info or suggestions is much appreciated??

You cannot get another OPT for the same level of degree (in this case your 2nd Masters).Since you are alrady counted on the H1B cap in 2009, you wont have to worry about the quota. If you used 1 yr in H1, then you have 5 more yrs remaining. The total yrs in H1b will still be 6 yrs, so any time you used up will be decreased. You will get your next h1b for 3 yrs and 2 yrs after that if you have used up 1 yr of H1b in 09. The process for applying H1b is the same as you did before except that you just would not be subject to the quotas. This is from my personal knowledge. Please correct me if I am wrong.