You can get the most out of your HD if you take some extra steps. The sad part is it will cost you money.
What I use to beat the 128 GB limit is the intech hi-cap driver. Works like a charm. Go to this link to check it out, it's $25. You can also buy the entire Speedtools utilities (I also own them) for $90. They perform some basic maintenance and do some other cool things. You can read about them individually at this link-
http://www.speedtools2.com/ATA6.html
You could go the route of getting an ATA pci card...but I doubt you need it, nor do you need to take up an entire precious pci slot. You've only got three, use them wisely. The ATA hi-cap driver would be my recommendation.
For more info on the 128 GB limit, you can read these Apple informational documents-
http://docs.info.apple.com/article.html?artnum=86178