Will 6tb drives work on a 2009 mac pro?

http://eshop.macsales.com/item/HGST/0F18335/

According to the compatibility section lower on the page, they will work. However, you might want to format them using Snow Leopard's Disk utility, unless you want everything to be Core Storage. Also, I don't know if the formatting problems introduced in Mountain Lion have been fixed yet:

http://forums.macrumors.com/showthread.php?t=1661024

You would hope that it's been fixed, but there is a sad tendency recently for problems to persist unfixed through OS "upgrades".

There is still a Bug in Disk Utility's ERASE function since 10.8.4, which makes drives over 2.2TB ERASEd internally unusable.

Use a different version for the ERASE. Anything after 10.4.6 should do fine, but the 10.6 DVD is simple.

Or install temporarily in an External Enclosure and use any version for the ERASE.

Some drives with capacities above 3TB have reneged on the length allowance for bottom-entering screws. There is not enough room for the standard sled screws directly adjacent to the platters, so the sled screws must be shortened. You could also try putting a washer under the screw-head.

Hard Drive mounting screws are SAE (American) thread, size #6-32 threads/inch.

DVD mounting screws (and 2.5-in hard Drives and SSDs) are Metric Thread, 3mm diameter, I think they are 0.5 mm/thread pitch.