This is a list of every single bill for which there was a difference, including those where only one of the two did not vote. These were taken from merged list of all votes by each candidate as listed by Project Vote Smart.
The first letter represents Hillary's vote, the second represents Obama's, and an X represents 'no vote.'
Y-N - Nov-05 - Tax Reconciliation Bill: Vote to Extend Tax Cuts
Y-N - Aug-06 - Gulf of Mexico Energy Security Act of 2006: Vote to Expand Oil Drilling in the Gulf
N-Y - Jun-05 - Appoint Thomas B. Griffith, US Circuit Judge
N-Y - Jul-05 - Energy Policy Act of 2005: Vote for Clean/Alternative Energy Policy
N-Y - Jul-06 - USEMA Amendment: Vote to abolish FEMA, replace with USEMA
N-Y - Jul-06 - Firearm Confiscation Prohibition Amendment: Vote to protect right to bear arms in an emergency/disastor
N-Y - Sep-06 - Cluster Munitions Amendment: Vote to prohibit any funding from going to cluster bombs
X-N - Mar-05 - Bankruptcy Reform Bill: Vote to increase the difficulty of claiming bankruptcy
Y-X - Apr-05 - Future Military Funding for Iraq Amendment: Vote for non-binding agreement about how military funds are categorized
Y-X - Jun-05 - Appoint Richard A Griffin, US Circuit Judge
Y-X - May-07 - FDA Drug Import Certification Amendment: Vote for a certification of imported prescription drugs
Y-X - Jun-07 - Attorney General No Confidence Vote: Vote so that a fillibuster can't be used for the vote of no-confidence for Attorney General Gonzales
Y-X - Jul-07 - Sense of the Senate on Guantanamo Bay Detainees: Vote that the Guantanamo detainees not be released on American soil or transferred to American facilities
Y-X - Jul-07 - Student Loan Lender Subsidy Cuts and Student Grants: Vote for various improvements to the student loan regulations (and makes it unlawful to carry out a death sentence on a pregnant woman?)
Y-X - Jul-07 - Department of Homeland Security Appropriations: Vote to confirm budget for Dep't of Homeland Security
Y-X - Jul-07 - REAL ID Funding: Vote to fund the REAL ID project where a national identification card is required for every citizen
N-X - Sep-07 - Expressing Support for General Petraeus and All Members of the Armed Forces: Vote to show support for the armed forces
Y-X - Sep-07 - Expressing the Sense of Congress Regarding Federalism in Iraq: Vote to support the opinion that Iraq work toward a loose federalist state and that the Iranian Revolutionary Guard be considered a terrorist organization
Y-X - Sep-07 - Expressing the Sense of Congress Regarding Iran and the Islamic Revolutionary Guard Corps: Vote to support the opinion that the United States should use its military, diplomatic, economic, and intelligence instruments to combat Iranian activities inside Iraq that are designed to destabilize Iraq
Y-X - Oct-07 - Border Fence and Customs Appropriations: Vote to appropriate 3 billion dollars to secure the Mexican border by means of a fence and electronic detection equipment
Bills that Clinton voted on before Obama became a Senator, but has since either expressed or implied disagreement with, or that do not typically represent the actions of a democrat:
Sep-01 - Military Force Authorization Resolution: Vote to allow the President to use force against nations that harbor or aid terrorists
Oct-01 - USA Patriot Act of 2001: "Vote to pass a bill that grants law enforcement more authority to search homes, tap phone lines, and track internet use of those suspected of terrorism for four years."
April-02 - Securing America's Future Energy (SAFE) Act: Enhance energy conservation and raise auto mileage standards.
Oct-02 - Use of Military Force Against Iraq: The big one.
Jul-03 - Energy Omnibus Bill: Vote to enhance energy conservation and R&D and allow tax breaks for energy production and conservation
Oct-03 - Healthy Forests Restoration Act of 2003: Vote to authorize $760 million per year to prevent forest fires and limit judicial reviews of established protection rules.
To sum it up: Don't let the media tell you that there is no difference between the candidates. Many of these bills are quite substantial and the votes in one way or the other, (and sometimes the lack of a vote at all), are extremely telling.