This question needs a "qualifier". Such as "for teams with at least 10 appearances"... As it stands, there are several teams with a 0% winning percentage. Most have attended 5 or less bowl games and some have never attended. http://kiko13.com/cflrankings/allrecords.htm
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As of the start of the 2007 season, for division 1A college football teams that had played at least 500 games total, the worst winning percentage belongs to Kent State University whose win loss record is 294-467-28 for a winning percentage of .390. The division 1A team with the most all time losses is Northwestern University whose all time win loss record is 453-604-44 for a winning percentage of .431.
As of the 2008 season, the Division 1-A team with the worst winning percentage that has played at least 300 total games is Kent State with an all time record of 297-476-28 for a winning percentage of .388. Florida International University began playing football in 2002. Their all time record coming into the 2008 season was 16-52 for a winning percentage of .235.
Unfortunately it was my favorite team of all time Oregon state university who form 1971-1998 had all losing seasons 28 in a row. they turned the corner in the year 2000 and posting a 12-1 season were ranked #4 in the nation and went on to beat Notre dame in the fiesta bowl. And are now ranked in the top 25 nearly every year!