Normally I would break down a television show this long with a episode by episode breakdown within each season. However, since this is a Sit-Com with very few deaths, I am going to encapsulate the particulars in a single entry.
There is a death of a small coffee shop owner about mid way through the series that will not be counted as his death is revealed within the time frame of the episode, but occurs outside of it.
Season 6 episode 13: Marshall’s dad dies of a heart attack
Season 9 episode 6: The minister dies in front of Barney and Robin
Season 9 episode 16: Emily(the mother from how I met your mother) find’s out over the phone that her boyfriend died.
Season 9 episode 24: Emily dies. This is a tough one. Normally I wouldn’t include this as it is unclear exactly when this occurs and it is not on screen. But since the last episode takes place over a very large time frame and this character is pivotal to the show it will be included.