The Dac is the same in all versions, so they will all sound the same in principle if used in equivalent manners. Yet there are some differences other than the obvious usb input in the usb version and the pre (+usb) in the pre version. For that, see the info in their site or give them a call.
I have recentlly bought the Dac 1 pre (US1600) due to its greater versatility. I have compared the dac section with the Headroom Micro dac (around US600) and the Bel Canto (around US2800). Let me just say that I'm very satisfied with the Benchmark. If you're between the Bel Canto and the Benchmark let me suggest the following. Both are great dacs and I believe that in terms of sound, the decision between one or the other would be idiosyncratic. The Bel canto looks much better and it is much more robust. That said, the Benchmark costs 1000 dollars less, has a headphone amp (the merits of which deserves a separate paragraph), and produces a better result with computers and cheap transports (DVD, CD, PS3, etc). Benchmark people also claimed to me that cabling – and believe it or not source – makes no difference with the dac1. For the technical explanation, which I'm not really interested, call them. As one should expect the Bel Canto will be more refined if used with their own cd transport, or something like that; however, the refinement would only be there if it is played through an equally refined amp, speakers, etc. Again, we would be talking completely different budgets. The comparison would be entirely unfair were it not for the fact that when we listen to both and think of the extra money necessary to make the Bel Canto top the Benchmark, we understand that one would only rationally buy the Bel Canto over the Bencjmark because of the former's appearance.
Other Dacs considered: Lavry, Grace, Apogee. All good stuff. Question here in my opinion is less "which is has the best sound" than "which is the most versatile". Perhaps this is why the Benchmark is so successful.