I've been using a mini-itx build (C60M1-I) for about two years now. I am close to filling up my fifth drive and would like to expand to something a little bigger. I recently picked  up a RSV-L4411 and am trying to decide what motherboard to use. I have a spare G1610 laying around and I would like to ideally uses all 12 of the drives in the case. Any recommendations?

This would work nicely -- has 6 SATA ports, with plenty of expansion slots to add another controller to easily expand to 12 drives:

 

http://www.newegg.com/Product/Product.aspx?Item=N82E16813131837

So if SATA ports and expansion slots are all to look out for, would this be fine?

 

http://www.newegg.com/Product/Product.aspx?Item=N82E16813157304

 

I use unRAID mostly for storage, nothing too fancy.

Yes, that motherboard will work fine.  A slightly lower-end chipset, but nothing that would impact the performance of UnRAID.