Good question! Here's the answer:
I generally use Vote Gopher for these purposes. You can compare candidates by issue, and they give you quotes to back it up. Issues 2000 (a.k.a. On The Issues) does the same (yes, it's updated to 2008) and is more extensive, but for the major issues, I find Vote Gopher more user-friendly.
My favorite site, though, is Open Secrets, which logs all monetary transactions made by the candidates (from the initial donation to where the money is spent). A great insight into the world of political fund raising, and where the money goes.
But if you want to compare the candidates side-by-side on one sheet of paper, I suggest getting a back issue of the New York Times from December 30. On pages 16-17 of the National Section (the A section, in this case), there is a full, broadsheet chart that includes the positions of all the major candidates from both parties (that means no Duncan Hunter, Dennis Kucinich, and certainly no Mike Gravel) on some of the main issues--Iraq, Health Care, Taxes, Detainees, Interrogation, Immigration, Energy and Climate Change. It's not perfect, but it's the easiest way to compare the candidates. And if you can't get a hold of that, the Times has a nice section with the candidates' biographies, web sites and relevant articles.