The Abraham Lincoln Assassination research site, operated by history teacher Roger Norton, is by far one of the best sites on the topic. It covers a wide variety of information in a very detailed manner. In addition it has sister sites devoted to specifics of the individuals, Abraham Lincoln and Mary Todd Lincoln.
The Boothie Barn is a blog devoted to deep research into the Lincoln Assassination and the lives of all involved. Run by teacher Dave Taylor, it's one of the most fascinating sources of information on the topic and Dave never fails to enlighten his audience with newly found information. Dave is also a tour guide on the John Wilkes Booth Escape Route Bus Tour, organized by the Surratt Society, and he is consistently updating his blog with the wealth of information he uncovers.
This site is managed by Ford's Theatre and brings together a wealth of newspaper articles, first hand accounts, and personal letters touching on many different aspects of Lincoln's death and assassination. As stated on their website, "the goal of the project is to localize and personalize the story of the Lincoln assassination for people around the United States and world."
The Lincoln Log is a wonderful resource for anyone interested in the daily and hourly activities of Abraham Lincoln. The website provides "a daily chronology of the life of Abraham Lincoln", by allowing the user to search for any date from President's birth to his death. Each log note is sourced for further verification and research.
While not solely devoted to the assassination, Mr. Lincoln's White House, has a vast amount of information regarding Abraham Lincoln and his presidency. It's important to understand Lincoln as a man and the era he lived in to fully capture the tragedy of his death.
This website has taken on the massive undertaking of digitizing all the federal records of Abraham Lincoln Presidential Administration. Checkout their massive compilation of documents, maps, political cartoons, records and more.
The National Museum of Health and Medicine in Silver Spring Maryland has a current exhibit entitled "HIS WOUND IS MORTAL; IT IS IMPOSSIBLE FOR HIM TO RECOVER" - THE FINAL HOURS OF PRESIDENT ABRAHAM LINCOLN". This exhibit details the autopsy of Abraham Lincoln and items on display include the surgical kit used in the autopsy of President Abraham Lincoln, as well as the bullet that killed Lincoln and fragments of the President's skull.