On WAR in Iraq, Afghanistan, Middle East (Foreign Policy):
McCain "Supports Bush's surge, in fact, calls for more additional troops than Bush recommends. Has been quoted as saying he is willing to stay in Iraq for 100 years. Obama,as a state senator, he spoke out against Iraq war, before the war started. Has long favored a phased withdrawal."
On Civil liberties: 
McCain voted for the PATRIOT act and it's revisions. "He generally opposes the interests of the American Civil Liberties Union." Obama voted against and later for bills to reauthorize the PATRIOT Act. "Let me be clear: this compromise is not as good as the Senate version of the bill, nor is it as good as the SAFE Act that I have cosponsored. I suspect the vast majority of my colleagues on both sides of the aisle feel the same way. But, it's still better than what the House originally proposed. This compromise does modestly improve the PATRIOT Act by strengthening civil liberties protections without sacrificing the tools that law enforcement needs to keep us safe." --February 16, 2006 Source. Obama supported the interests of the American Civil Liberties Union 83 percent in 2005-2006. "Senator Obama is a member of the Senate Homeland Security and Governmental Affairs Committee and has supported efforts to base homeland security spending on risk rather than pork-barrel politics. He has also introduced legislation to strength chemical plant and drinking water security and to enhance disaster preparedness." -Campaign site
Social Security:
McCain would allow workers to invest a portion of their payroll tax in private accounts which they manage themselves. Senator Obama supported the interests of the Alliance for Retired Americans 100 percent in 2005.
Stem cell research: 
Both candidates support federally funded stem cell research.
Same-sex marriage: 
McCain has mixed responses from favoring to opposing same sex marriage, seemingly in favor of legal agreements but not marriage or unions. Obama favors civil unions, but opposes same sex marriage.
Free Trade: 
McCain in favor, Obama mixed voting record.
Abortion: 
MCain mostly pro-life, except in some circumstances. Obama pro-choice.
Capital punishment: 
McCain supports the death penalty, Obama does as well - but questions the legal system.
Medical Marijuana: 
McCain opposes legalization, Obama in favor if proved useful in treatment.
Gun control: 
McCain is mixed with wanting moderate gun control, Obama wants strict gun control.
Health care: 
McCain opposes universal health care, Obama supports it.
Immigration: 
McCain and Obama support amnesty/permanent legalization for illegal aliens and temporary legalization for illegal aiens as guestworkers Source
Education:
MCCain Supports vouchers, Obama opposes them.
Here is basic questionnaire to help you pick if you haven't already, from 2decide.com, rather basic, but it gets the job done.
HERE is a really cool questionnaire where you can select a candidate and whatever issue you want to see their views on.
The Candidates on the issues
