1) Drive spindown isn't really desirable IMHO. I disabled it completely and disabled all power/acoustic management on the drives.
Reason being: Hard-drives have no physical wear apart from the brushless DC motor while running. However, when the drive is turned off or enters a lower power state the head is parked on the platter which wears out the head and also wears the platter.
Brushless DC motors are some of the most reliable motors on the planet (can go for years and years without issue). You really should only consider it if you don't use your NAS that often or you really need to save on your power bill.
Drive life is actually longer if you keep it running in a environment with constant temperature VS. constant turning on/off and temperature fluctuations.
2) There really is only 1 choice IMHO: IBM M1015 (LSI SAS2008). On Ebay they go new for $60-$100 dollars. I'm not located in the US so I had to buy from a seller in Russia whom shipped to my country. Cost me $96. It does need to be flashed but there is a very good guide @ servethehome (google).
Once that is done it supports FreeBSD out of the box. Supports hot swap, S.M.A.R.T, drives greater than 3TB, SATA-6GB and LSI make controller chips for many hard-drives so it supports hard-drives very well (it might seem strange but some controllers do have issues with certain drives).
I've flashed mine without a BIOS, so it doesn't do any drive detections during POST. It is pretty much invisible until you reach the OS at which point it exposes the drives directly. Then there is the price, I challenge you... no.. dare you, find another controller with that feature list for a lower price (believe me I've tried).
I personally also tested a Highpoint RocketRAID 2720SGL with a JBOD/"IT" firmware, it however had the following problems: No hot swap support (a very loud alarm would sound once the drive disconnects and it never stops so that pretty much ruled out hot swap for me). It also isn't supported out of the box (requires using SSH and adding the driver to FreeNAS every time you upgrade). Lastly FreeNAS couldn't detect a disk unless I pre-formatted it, with any kind of file system (that to me was a deal breaker). Performance on the RocketRAID seemed the same however (only did quick tests before I sold it).
If however you aren't convinced, have a look for yourself:
http://blog.zorinaq.com/?e=10
