In the book, The Magic Numbers of Dr. Matrix, by Martin Gardner, the following parallels are given between the two presidents. Martin Gardner attributes this to a Dr. Irving Joshua Matrix. The last item is due to Terry W. Harmon. This was done as a satire on reading too much into coincidences.

bulletLincoln was elected president in 1860. Kennedy was elected president in 1960.
bulletBoth men were deeply involved in civil rights for Negroes.
bulletBoth men were assassinated on a Friday, in the presence of their wives.
bulletEach wife had lost a son while living in the White House.
bulletBoth men were killed by a bullet that entered the head from behind.
bulletLincoln was killed in Ford's Theater. Kennedy was shot while riding in a Lincoln convertible made by the Ford Motor Company.
bulletBoth men were succeeded by vice-presidents named Johnson who were Southern Democrats and former senators.
bulletAndrew Johnson was born in 1808. Lyndon Johnson was born in 1908.
bulletThe first name of Lincoln's private secretary was John. The last name of Kennedy's private secretary was Lincoln.
bulletJohn Wilkes Booth was born in 1839. Lee Harvey Oswald was born in 1939.
bulletBoth assassins were Southerners who held extremist views.
bulletBoth assassins were murdered before they could be brought to trial.
bulletBooth shot Lincoln in a theater and fled to a barn (a warehouse for cows). Oswald shot Kennedy from a warehouse and fled to a theater.
bulletLINCOLN and KENNEDY each has seven letters.
bulletANDREW JOHNSON and LYNDON JOHNSON each has 13 letters.
bulletJOHN WILKES BOOTH and LEE HARVEY OSWALD each has 15 letters.
bulletThe digits of 11/22 add to 6, and FRIDAY has 6 letters. If each of the letters in FBI are shifted forward 6 letters you get LHO, the initials of Lee Harvey Oswald. OSWALD has 6 letters. Oswald shot from the sixth floor of the building where he worked. The triple shift of letters from FBI to LHO can be expressed as 666.
bulletThe first public suggestion that Lincoln be the Republican candidate for president is believed to have been in a letter written to the Cincinnati Gazette on November 6, 1858. The letter was written by Israel Green. He suggested a ticket with Lincoln for president and John (Pendleton) Kennedy or vice president.

There is another comparison between two other presidents that were assassinated. It has not received as much attention as this one.