Can multiple/duplicate applications be filed to increase my chances in the lottery?

a)Two or more employers each file for you at the same time.

Yes

Just make sure not to mislead or misinform any of the employers about the other petition.  

b) One employer files two petitions for you.

Though there is no specific law to disallow this practice, it might be considered an exploitation of the system. Few employers did that last year.

 Can I file under both Master’s and regular quota?

Right now it seems that you can BUT USCIS is drafting and can come up with a new regulation to address duplicate filing any day now. This new regulation is expected to address all multiple filing issues.