Tricky question since there are all kinds of ways people try to distort the counting of wins and losses (div 1a vs others, etc). However, Amos Alonzo Stagg (Sr.) had 190 losses and no coach was recorded as having more since he started losing games back in 1892.
As of September 22, 2007, John Gagliardi from St. John's University in Collegeville, MN has 447 wins, the late Eddie Robinson has 408 wins, Bobby Bowden 359 wins, Joe Paterno 354 wins, Amos Alonzo Stagg 340 wins.
Amos Alonzo Stagg. Depending on the source, he compiled a record of 340-201-36 (Source: McClatchy Newspapers) or 314-199-35 (Source: Wikipedia), but either way it's far ahead of Hayden Fry's 178 losses in a total record of 232-178-10.
George Jewett played at the University of Michigan from 1890-1893. He played against teams coached by Amos Alonzo Stagg and John Heisman. After he graduated, he attended Northwestern and played for them as a grad student.
As of December 10, 2011, the longest streak is 44 games by the University of Wisconsin at Whitewater. They currently hold 2 consecutive NCAA Division III championships and will vie for a third in a row on December 16th at the Amos Alonzo Stagg Bowl.