The Southwest website suggests that links to the 50,000 point Chase Southwest Rapid Rewards Premier card & the Chase Air Tran credit card with 32 credits by will end soon.
I don’t know if the non-affiliate offer will disappear as well (I’d guess not, but I don’t have any inside information). But I wouldn’t worry about applying for the Southwest card now if you didn’t already plan on applying for it.
That said, it is rare to see all 4 Southwest cards offer the 50,000 point bonus at the same time, so if you’re looking for a specific card (Plus vs. Premier etc.), it could be best to evaluate your options.
As I wrote before in “How to Fly Free for Two Years on Southwest!” two Southwest 50,000 point credit cards can get you (hopefully) up to 2 years of free flying on Southwest with their Companion Pass. Or at the very least ~$1,670 in Southwest flights if the points earned from the credit card stop counting towards the Southwest Companion Pass.
I just received my two Southwest cards, so I’ve got my fingers crossed for my Companion Pass in 2013!
Chase and Southwest have had the 50,000 point Southwest offer every 2 or 3 months for over 1 year, so I wouldn’t worry about missing out on the cards now, because they almost certainly will be back. As always, do what makes sense for you!