I personally do not like using an on-board raid system due to seeing many times someone's board die and being unable to do anything about a degraded raid when they cannot find a replacement motherboard with the same raid chip on it. PCI/PCI express raid cards can be costly, especially if you are using more than 4 drives on the card, but the chips on them are easier to find replacements for if the card dies. The NAS system idea is a good cost effective idea and an energy efficient system can cut back on energy costs more so than raiding in a desktop would.
Here are a few points that I like to take into consideration:
1. Good airflow-A cool drive is a happy drive and heat is the third worst thing for it. (top two being power surge and dropping the drive)
2. Hot-Swappable-If the drive has a problem, how easy is it to replace or test.
3. Functionality-A nice user interface over the web is great, but you want to know that it has all of the features you need.
3. Stability-There is nothing worse than losing your raid when you have a lot of data that you cannot afford to lose. Make sure you can trust the manufacturer of your raid system. If they constantly get bad reviews on their products and service, you do not want to buy their equipment.(I prefer Synology, Highpoint, and Thecus NAS systems)
With all that in consideration you want to look at your price range. As you may already know, you are only going to see cards and NAS systems with 1, 2, 4, 6,....etc ports and a raid 5 will take at least 3 drives to do this.
So now that we have this out of the way, lets look at what this is going to be for. For high performance data transfers you will want at least a 7200RPM drive and if you have the money to burn, a couple of SAS drives. I do not recommend this for a NAS system unless you are using a rack-mount system and more than one gigabit port or have it in your desktop/server on a raid card. USB 3.0 has an estimated speed of up to 625MB/s(300MB for eSata), but you wont find too many USB 3.0/eSata enclosures that support raid 5 and SATA II does not transfer any faster than eSata.
A normal NAS system has only one gigabit port and will not be able to transfer data faster than ~70MB/s making it a good solution for raided data storage. (My NAS system only does ~45MB/s ) If you do decide to go with a gigabit NAS system you can go with 5400 RPM drives as they consume less power, are quieter, and produce less heat, as well as they are cheaper and you are only limited by your network's speed.
I hope this helps you in making your decision. If you are purchasing a card make sure you look at the maximum transfer speeds as not all of them transfer at full speed, but still have most of the other features.
Highpoint 4 Port Raid Controller Card
Highpoint 8 Port Raid Controller Card
Thecus 4 Bay Diskless NAS server