Flaherty died March 16 of a heart attack at his home in Belmont, about 20 miles south of San Francisco, family members said Friday.
Flaherty came up with the idea of indexing Web pages that made the AltaVista search engine one of the most popular Internet search tools in the mid-1990s.
"He was such a warm and loving man, and he was exceptionally smart," his brother, Michael, said Friday. "It's just uncanny to find someone with that much intellectual power but that much warmth, too."
Flaherty was working as a research engineer at Digital Equipment Corp. in Palo Alto when he teamed up with two other staff researchers in 1995 to develop AltaVista's technology.
The Web site was made public in December 1995 and within weeks was processing several million searches a day. It was spun off from Digital Equipment as a private company in 1999.
Flaherty served as director for technical strategy at AltaVista until leaving in 2000 to work in management consulting. At the time of his death, he was vice president for product development at TalkPlus, a telecommunications software company in Menlo Park.
Born in Milwaukee and raised in Minnesota, Flaherty earned a doctorate in electrical engineering in 1994 from Stanford University and never quite shook his Midwest roots despite his success in Silicon Valley, Michael Flaherty said.
"I never saw him taking to the more cutthroat lifestyle in Silicon Valley," his brother said.
He is survived by his wife, Natasha Flaherty of Belmont; his parents, James Sr. and Ruth Flaherty of Fargo, N.D.; and four brothers.
A funeral mass and burial is scheduled for Tuesday in Fargo.