I would say, without a doubt, yes. SATA-III has a maximum throughput of 6.0 Gb/s, while SATA-II has a maximum throughput of 3.0 Gb/s. If we take into account the fact that both use 8b/10b encoding, both buses max out at a reasonable 600 MB/s and 300 MB/s.
I personally have the 120 GB model of the OCZ Agility 3, and it is running on my motherboard's native SATA-III port. During benchmarking, I hit well over 500 MB/s actual transfer rate, so you would be limiting your maximum transfer speed with the SATA-II controller.
If you do wish to upgrade with a new PCIe SATA-III controller, please see my answer to this question, titled "Adding a SATA 6 Gbit/s PCI Express controller card?". Summarizing what I wrote there, let us assume you use a worst-case PCIe 1x controller card. Your maximum throughput would be roughly 450 MB/s, or 1.5 times what you have now.
Whether or not you notice the difference in those transfer rates depends on you as a user, and what your purposes for the drive are. Even if your drive was capped-out at 300 MB/s, it still has nearly zero seek time compared to a conventional mechanical hard disk, and that's what most users will primarily notice.
After the whole seek time debate (because lower is always better), it depends on what you have stored on the drive and what you use it for (e.g. bandwidth intensive tasks like video editing, or low bandwidth tasks like internet surfing). That itself will dictate whether or not the increased bandwidth is warranted in your case.
Hey, thanks! :) Would you be so kind to point me to a sata3 controller you consider a good bang for the buck? – Pitto – 2011-07-14T08:21:20.277
@Pitto shopping recommendations are disallowed on this site, but I have seen a few at good prices from Star Tech or Bytecc. They have ones with 1 internal and 1 eSATA ports, or ones with just two internal ones. They both have a few different ones listed on their sites, but I always see them cheaper at various retailers. If it has what you need, I would just go for the one on sale (AKA cheaper). An example of one of these can be found from my answer to the other question mentioned above.
– Breakthrough – 2011-07-14T10:35:11.223I didn't want to push you into illegal but I've read that ONLY intel controllers are good so I thought asking to understand if you'd say the same or suggest also other companies :) – Pitto – 2011-07-14T11:42:24.547
@Pitto, I'm a fan of Intel controllers myself, but I don't know if they are offered on any PCIe-based solutions (only on motherboards). My second pick would be a Marvell-based controller (which some motherboards also use as an additional SATA controller). Another good one is from JMicron. Again though, these are just "big tech names" and don't really indicate the throughput you will actually get in the end. – Breakthrough – 2011-07-14T13:55:18.117
@Pitto did you end up purchasing a PCI-e SATA controller? I would be interested to know what brand/model you went with, and if it works well. I forgot to say that shopping recommendations are only off-topic with respect to questions and answers - in a comment like this, it would be appropriate (esp. considering we're just sharing an experience as an end-user). – Breakthrough – 2014-03-15T01:20:16.383