I moved into my friend's apartment in September 2006 in place of her roommate who was moving out. My name was never on the lease. I paid the previous roommate her half of the security back under the conditions that when myself and the present roommate moved out I would get my security back. It was understood that we would reside there until the end of May, 2008 which would have been the duration of the rental agreement. On May 2nd, I received an email from my roommate stating that she and her boyfriend would be taking over the lease as of May 1st and would be doing a month to month until their new place was ready. I told her that "our lease" didn't end until May 31st and that I paid May's rent already. I explained that I would like to split the rent three ways because it was only right being that there would be three persons residing in the apt in the month of May. I also stated that I would like my portion of the security I paid back being that someone else was taking over the apartment. She never acknowledged reimbursing me my portion of the rent. I chose to make a stop payment on my May rent check being that I didn't agree to a third party residing in the apt, nor was I being compensated fairly. She also stated she has nothing to do with the security therefore wasn't giving my portion back to me although someone else was taking my place. She is now suing me in small claims court for May's rent plus late fees. Being that I'm not on the lease nor did I have any written agreement, does she have a case?

You're responsible for the rent until the date you moved out, so she has a case for that. However she is responsible for refunding your share of the security deposit. Make sure you file a counterclaim for the security.

If you already paid her that rent for may you should have a copy of the emails stating she was moving in and such AND a copy of your rent check.
She may be suing you but file a counterclaim if you paid the deposit in a check.

As Lisa pointed out you are responsible for the rent until you move out. But in addition to counter suing for the deposit, you should counter sue for a reduction in the rental because of a third roommate having moved in.