Definitely 5D2... Self Cleaning Sensor (a big factor for me, I often have to shoot in dusty conditions), Micro Adjust, Live View, 21MP/14 bit vs 16MP/12 bit, Digic 4 vs dual Digic 2 processors, option to use grip... (or not, if you're going hiking with the camera). ISO 25600 (though honestly I rarely use above 6400, unless I'm going to convert to B&W) vs 3200. 2"/230K LCD vs 3"/920K LCD. 2008 model vs 2004 model.
5D2 and 50D compliment each other very well... Controls, layout, menu are very similar. Just few quirks (the replay button on one is the same place as the erase button on the other... I worried about that, but never actually had a problem switching back and forth between them). MGiddings is right, default color rendition of 50D and 5DII is very similar. At times I shot with 50D and later during post processing mistakenly thought I'd shot with 5DII until I checked the EXIF.
On the other hand, the 1Ds2 is built like a tank, has a much better AF system for moving subjects, has 100% viewfinder vs 98%, dual memory card slots (though one is CF and the other is SD) and is more customizable. It also has 1/250 flash sync vs 1/200, and +/- 3 stops of Exposure Compensate vs +/- 2 stops.
The 1Ds2 has 200K rated shutter and the 5DII has 150K... Not all that different.
1Ds2 uses a 21 zone metering system, 5DII uses a 35 zone. The 1Ds2 has slightly smaller spot meter area: 2.4% vs 3.5% of viewfinder area.
Scanning over the specifications (at the Canon Camera Museum), 1Ds2 appears to have AF point linked spot metering too... That was a feature I really enjoyed having on my old EOS-3 and haven't had on any model since (7E, A2E, 10D, 30D, 50D, 5DII, 7D). Essentially, rather than simply being locked just at the center, spot metering "follows" the selected/active AF point around the viewfinder area... On EOS-3 this wasn't available for all 45 AF points, was only possible when limiting the camera to using 13 AF points via a custom function (I'd assume the 1Ds2 is the same). I loved this feature though.
5DII has video capability, too... if you need it.