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. "The most important weapons in the U.S. arsenal are the men and women of American armed forces. John McCain believes we must enlarge the size of our armed forces to meet new challenges to our security. For too long, we have asked too much of too few - with the result that many service personnel are on their second, third and even fourth tours of duty in Afghanistan and Iraq. There can be no higher defense priority than the proper compensation, training, and equipping of our troops." Read more here.
Obama,as a state senator, he spoke out against Iraq war, before the war started. Has long favored a "phased withdrawal." "Our country's greatest military asset is the men and women who wear the uniform of the United States. When we do send our men and women into harm's way, we must also clearly define the mission, prescribe concrete political and military objectives, seek out advice of our military commanders, evaluate the intelligence, plan accordingly, and ensure that our troops have the resources, support, and equipment they need to protect themselves and fulfill their mission." -Barack Obama, Chicago Foreign Affairs Council, April 23, 2007. Read more here.
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. McCain's campaign site did not have a subject devoted to social security.
Senator Obama supported the interests of the Alliance for Retired Americans 100 percent in 2005. "We… have an obligation to protect Social Security and ensure that it's a safety net the American people can count on today, tomorrow and forever. Social Security is the cornerstone of the social compact in this country… Coming together to meet this challenge won't be easy… It will take restoring a sense of shared purpose in Washington and across this country. But if you put your trust in me — if you give me 'your hand and your heart' — then that's exactly what I intend to do as your next President." — Barack Obama, Speech in Des Moines, IA, October 27, 2007. Read more here.
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 is 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. "John McCain believes that the right of law abiding citizens to keep and bear arms is a fundamental, individual Constitutional right that we have a sacred duty to protect. We have a responsibility to ensure that criminals who violate the law are prosecuted to the fullest, rather than restricting the rights of law abiding citizens. Gun control is a proven failure in fighting crime." Find more about McCain's stance here. Obama wants strict gun control.
Health care: 
McCain opposes universal health care, rather he calls for reform, 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.
Candidate Comparisons, compare the remaining candidates
