The majority of people prefer custom PCB cards, but I personally like reference cards. I have two EVGA 980 Ti FTW (custom PCBs & fans) and I have one EVGA 980 Ti (4992) reference cooler. Ideally, if I was getting a single 980 Ti, I'd go for a custom cooler, but with two cards, I'd be inclined to get two reference cards. I like that the heat is exhausted out of the back of the card, instead of straight into the case. Also, I know that I would buy reference if I was getting a custom water loop. I have no experience with that yet, so I don't know if it's possible to install water block with non-reference cards. When Pascal comes out, I will be buying four Pascal version of 980 Ti's.
Besides, do you have any other options besides reference? Can you get a rain check from EVGA and get a custom card at a later date, or is it reference or nothing?