I own a Calypso with well upgraded tubes. I love this preamp, in my system it is a very good addition. However, if my budget were not a factor, I would have gone with the Ref 3.
In my experience the Ref. 3 is more resolving and detailed over the Calypso (but the Calypso is plenty detailed/resolving for me, I run Krell amps and Wilson speakers so I like resolving and the Calypso adds just the right amount of tubed warmth without compromising the resolution I like).
There are not very many preamps I would prefer over the Calypso, but the Ref 3 would be the first that comes to my mind. I think both are excellent preamps and I do not feel the Ref 3 is anywhere close to twice the price better than the Calypso.
I think the Calypso delivers better flexibility as it responds better to tube rolling (a requirement for the Calypso anyway). I must admit that I don't really have much experience with tube rolling the Ref 3, just what I have read.
Again, the key to the Calypso is the tubes, you should add $1,000 to the price to put in the best tubes for this unit - factor that aspect into the purchase price.