If I am planning to upgrade my Macbook Pro 13" (Late 2011) with a 7200RPM Hard drive, should I get a SATA 3Gb/s or SATA 6Gb/s drive?
Short answer: it doesn't matter.
Longer version: Either will work fine. SATA is backwards compatible, so SATA 6Gb/s drives will work on SATA 3Gb/s interfaces and vice-versa. The 2011 Macbook Pros have 6Gb/s ports for the HD (some in the optical bay as well). However, no mechanical hard drive can come close to maxing out SATA 3Gb/s speed, so you'll see no difference from a 6Gb/s drive or interface. It makes a difference with SSDs, but with hard drives, it's merely marketing.
As a conventional hard drive wouldn't come close to 3GB/s, I say save some money and go for the cheaper 3GB/s one. If you have money to splash then instead I suggest you go for a SSD, because that would really lift your MBP's performance. It doesn't have to be as large and your current drive, because you can use your current drive as a external one by getting a SATA to USB casing somewhere to take some of the load off.
Another option, if you don't really need the optical drive is to get an adapter and put a big conventional drive in the optical bay (via an adapter such as from OWC) and then put a 6Gb/s SSD drive in as your boot drive. Super fast, and very useful. I'm finding optical drives to be less important than they used to be unless you're a gamer.