I'm far from an authority on presidential history. I certainly do not have the breadth of knowledge to do a credible and comprehensive list. Admittedly, most presidents prior to the twentieth century kinda fell to my intellectual peripheral after history classes in secondary school ended. Therefore, full disclosure, my list will include mostly twentieth century presidents, as those are the ones I am most familiar with.
- Harry S. Truman (1945-1953): He tops my list for dropping two atomic bombs on the Japanese cities of Hiroshima and Nagasaki. Even outside of the almost instantaneous deaths of thousands (mostly civilian), there is the near half century afterwards of deaths associated with those bombings. Also, Truman oversaw the Korean War, which seems to have fallen through the cracks of history. I find that peculiar given the death toll on all sides. Not to mention, that was an undeclared war.
- Abraham Lincoln (1860-1865): Some, I'm sure, will oppose this one quite vehemently. However, he presided over the worst conflict in American history, as well as was an awful president on the civil liberties front (going after civilians, his political opponents and newspapermen in the Northern states).
- Franklin Delano Roosevelt (1933-1945): He exacerbated the Great Depression and instituted economic policies and institutions which are still with us today that are doing harm to the economy. Lincoln contributed to this notion of a strong central-state and FDR took that notion and greatly expanded it to include an enormous bureaucratic government domestically and abroad. Then there is the obvious point about Japanese, Italian and German interment during World War II. Moreover, FDR's attempt to expand the Supreme Court are dubious and a mark against his presidency as well. Hell, there was wiretapping going on, even back then during the War.
- Woodrow Wilson (1913-1921): Dude's a nightmare for libertarians. He oversaw the Federal Reserve, the income tax, brought us into World War 1 to "make the world safe for democracy" and was awful on civil liberties, which the latter seems to be a common theme thus far.
- George W. Bush (2001-2009): Where do I begin? He essentially built this awful "War on Terrorism" apparatus that included Abu Ghraib/torture, rendition, the negation of civil liberties, wiretapping, a perpetual global war, etc. Oh, and he invaded a country (Iraq) unnecessarily resulting in thousands of dead Iraqis, Americans and the like, as well as costing a shitload of monies. There's FEMA and Hurricane Katrina, Medicaid Part D, No Child Left Behind, bailing out banks, etc., as well. Additionally, there's the Plame leak that's awful.
- Lyndon B. Johnson (1963-1969): He didn't start Vietnam, but he oversaw the escalation of it, as well as the draft. I also find his "Great Society" to be right there with the Neal Deal as further government intrusion into the economy.
- Richard Nixon (1969-1973): Elected to end the Vietnam War, but instead continues it and bombs the shit out of Cambodia on top of that. Then there's Watergate and general corruptness. Plus, the War on Drugs begins with him, I believe.
After that, I'd probably have Ronald Reagan (mostly for Iran-Contra) and Barack Obama (for continuing/escalating the "War on Terrorism" apparatus that Bush began, continuing the bailouts, and not prosecuting anyone in the Bush administration).
For comparison sakes, this link here has the top listed presidents and the bottom listed presidents in U.S. history.
I get a kick of the fact that Lincoln and FDR are in the top three for "best" while they are in the top three for "worst" on my list. Likewise, Truman and Wilson also make an appearance in the top ten.
And just for fun, I'd say Calvin Coolidge (1923-1929) is my favorite president of the twentieth century, if I had to pick one.