I was in the same situation. However, you don't want to call Southwest, you have to get in touch with AirTran. There was a message on AirTran's website - not sure if it's still there - that AirTran's gift certificates will not convert to Southwest LUV vouchers, so that's not an option.

People on here have reported that they were successful in having AirTran deposit credits in their A+ Rewards account that are transferable to Southwest and can then be used to book awards. I didn't get the same offer, however, when I spoke to an AirTran agent back in April, they told me any outstanding gift certificates would be refunded. And that's what they did with mine. I was told it can take up to 2 weeks.

My gift certificate was issued in January 2011 and the remaining balance was $220+ So, my advice to you is to get in touch with AirTran and ask them to get it refunded, now that it's known that AirTran's last flight is 3 months from now. You can easily let them know you don't plan on traveling in the next 3 months and would like to get a refund. Good Luck!