[1] He was honored on FAU's 20th Anniversary Team as a pitcher and utility player and in 2008 was inducted into the school's Baseball Hall of Fame.

[3] Murphy guided the Fighting Irish to a 318–116–1 (.732) record in South Bend, including consecutive trips to NCAA regional finals in 1992, 1993, and 1994.

Twice in that same decade, Murphy had teams finish in the top 3 in the country; a feat matched by only ten other schools.

Murphy's ASU teams were consistently present in the national top 25, including a streak of 100 consecutive weeks in the polls that lasted from 2000 until the middle of 2005.

His teams set an NCAA record of not being shut out in 506 consecutive games between 1995 and 2004, shattering the previous streak of 349.

The Arizona State athletic department was faulted for lack of institutional control, however, resulting in the baseball program being sanctioned and banned from postseason play in the 2012 season, as ASU was a repeat offender.

[8] For the 1988 Olympics, Murphy was replaced by former Northern Colorado Bears coach Tom Petroff as skipper of the Dutch team.

Under him, the Netherlands finished fifth with a 3-4 record, missing the medal round but managing to win against Cuba, which up to that point undefeated in Olympic competition.

Three of his players, Robert Eenhoorn, Hensley Meulens, and Evert-Jan 't Hoen, would go on to manage the Netherlands team in the future.

[13] On June 16, 2015, Murphy was appointed interim manager of the San Diego Padres after then-manager Bud Black was fired.

[16] On June 11, 2023, Murphy filled in as manager for an absent Craig Counsell, who missed the game due to his son's graduation.

[18][19][20] Before the 2024 season, most analysts and reporters predicted the Brewers would finish low in the NL Central due to Craig Counsell’s departure, the loss of key players including star pitcher Corbin Burnes, and Murphy’s limited experience as an MLB manager.