Unless you have the machine to handle it, I'd stick with the 3.0Gb/s drives. From everything I've read, 95% of the systems out there and that are being built, don't even use the full 3Gb/s of standard drives. Save your money and just look for a drive with the most cache you can get, that will help the most, IMO-and in others I've read. Also, If your looking into a SSD, make sure you do your reading. Unlike a standard "Disk" drive; you don't Defrag and have a handful of settings you have to set differently. The speed of a SSD is impressive though!
With a mechanical HDD (that is, NOT the new solid state SSD's) you will never get the disk mechanism up to that 6 Gb/s max burst speed capacity of the communication system involved, so the speed of the spinning disk operations (and its heads) will be the limit. Right now and into the near future, it will be hard to get those up to the speed of SATA 3.0 Gb/s, so that's all you will need for mechanical HDD's. For that reason I see no justification for paying extra for 6 vs 3.
HOWEVER, the Cache size is a different matter. It certainly is true that a 64 MB cache will speed things up over a 32 MB cache on many common types of applications. The difference may not be huge (it's less that the impact of 32 MB over 16 MB), but it is real. Try looking around here and on other sites for disk performance reviews that use actual measurements - not just speculation based on specifications and PR fluff - to see exactly how much difference the cache size makes, but be sure to compare devices that are as similar as possible except for the cache size. Then you can decide whether those differences are worth the price difference you are looking at. My ideal would be a modern SATA 3.0 Gb/s HDD with a 64MB cache 7200 rpm.
The difference is $10 though... SATA 6.0Gb/s isn't going to HURT me right? So at the very least, $10 for a bigger cache isn't that bad is it? Plus SATA 6.0Gb/s can definitely read the cache faster, if I'm not mistaken
SATA 6Gbit/sec won't hurt and it will read faster from the cache, but although it's the kind of difference you might be able to detect with the right kind of performance measurement you won't actually notice anything in typical usage. I personally wouldn't spend more money for it, but as long as it's not very MUCH extra money then go right ahead.
I think it's worth spending extra on a Motherboard with 6Gbit/sec ports because it's an investment in the future if you want to upgrade to a very fast SSD later on. But the speed of a hard drive is fixed by its density and spin rate, so if the drive isn't capable of utilizing the bandwidth today then there really isn't any potential future payoff for buying one with a faster connection.