If I were you I would buy a C3100 and a Symbol CF WiFi. That way you would have a new device(with a warranty depending on the seller up to 2 years), 128Mb Flash instead of 64Mb, 4Gb, Wifi, better keyboard (with dedicated row for numbers, Ctrl, Fn, Alt, Shift), jog wheel, 3.5mm jack instead of 2.5mm. But that's just me. I had a 6k and switched for a C1000(that may sound silly for some) because of the form factor, size, new device and better support from developpers.
As Adf said it really depends what you want. Ask yourself if you will mostly use it in portrait mode or landscape mode. Speed wise they are roughly the same. Battery wise there is more juice in the C3100. On the other hand the 6k is rock solid, has better/bigger screen, integrated WiFi, has a microphone so that you can use it for VOIP.
At the moment support from developpers is better for the 6k(SharpROM, OZ, PdaXROM, GuylhemROM) because the C3100(SharpROM) is so new. But I think that support from developpers will be good too for the C3100 in the future as it's close to a C1000 in terms of hardware. The 6K is not sold anymore, so it's hard to find accessories for it like the plastic cover screen, battery and the sled-battery(Power Mickeyl).
Hope this help.