Here's the list, as far as the AP poll's #1 vs #2 in the regular season (it's happened 17 more times in Bowl games, including tOSU's 1969 Rose Bowl win over #2 USC and the 2003 Fiesta Bowl triumph over #1 Miami):
Regular season football games between AP #1 and AP #2 (edit - updated 01/09/07):
Nov. 18, 2006 - No. 1 Ohio State 42, No. 2 Michigan 39
Sep. 09, 2006 - No. 1 Ohio State 24, No. 2 Texas 7
Nov. 30, 1996 - No. 2 Florida State 24, No. 1 Florida 21
Nov. 13, 1993 - No. 2 Notre Dame 31, No. 1 Florida State 24
Nov. 16, 1991 - No. 2 Miami 17, No. 1 Florida State 16
Sep. 16, 1989 - No. 1 Notre Dame 24, No. 2 Michigan 19
Nov. 26, 1988 - No. 1 Notre Dame 27, No. 2 Southern California 10
Nov. 21, 1987 - No. 2 Oklahoma 17, No. 1 Nebraska 7
Sep. 27, 1986 - No. 2 Miami 28, No. 1 Oklahoma 16
Oct. 19, 1985 - No. 1 Iowa 12, No. 2 Michigan 10
Sep. 26, 1981 - No. 1 Southern California 28, No. 2 Oklahoma 24
Nov. 25, 1971 - No. 1 Nebraska 35, No. 2 Oklahoma 31
Dec. 06, 1969 - No. 1 Texas 15, No. 2 Arkansas 14
Sep. 28, 1968 - No. 1 Purdue 37, No. 2 Notre Dame 22
Nov. 19, 1966 - No. 1 Notre Dame 10, No. 2 Michigan State 10, tie
Oct. 12, 1963 - No. 2 Texas 28, No. 1 Oklahoma 7
Nov. 09, 1946 - No. 1 Army 0, No. 2 Notre Dame 0, tie
Dec. 01, 1945 - No. 1 Army 32, No. 2 Navy 13
Nov. 10, 1945 - No. 1 Army 48, No. 2 Notre Dame 0
Dec. 02, 1944 - No. 1 Army 23, No. 2 Navy 7
Nov. 20, 1943 - No. 1 Notre Dame 14, No. 2 Iowa Pre-Flight 13
Oct. 09, 1943 - No. 1 Notre Dame 35, No. 2 Michigan 12
Edit - Here are all of the Bowl games between AP #1 and AP #2:
Jan. 08, 2007 - No. 2 Florida 41, No. 1 Ohio St. 14 (BCS Championship)
Jan. 04, 2006 - No. 2 Texas 41, No. 1 Southern California 38 (Rose)
Jan. 04, 2005 - No. 1 Southern California 55, No. 2 Oklahoma 19 (Orange)
Jan. 03, 2003 - No. 2 Ohio St. 31, No. 1 Miami 24, 2OT (Fiesta)
Jan. 04, 2000 - No. 1 Florida St. 46, No. 2 Virginia Tech 29 (Sugar)
Jan. 04, 1999 - No. 1 Tennessee 23, No. 2 Florida St. 16 (Fiesta)
Jan. 02, 1996 - No. 1 Nebraska 62, No. 2 Florida 24 (Fiesta)
Jan. 01, 1994 - No. 1 Florida St. 18, No. 2 Nebraska 16 (Orange)
Jan. 01, 1993 - No. 2 Alabama 34, No. 1 Miami 13 (Sugar)
Jan. 01, 1988 - No. 2 Miami 20, No. 1 Oklahoma 14 (Orange)
Jan. 02, 1987 - No. 2 Penn St. 14, No. 1 Miami 10 (Fiesta)
Jan. 01, 1983 - No. 2 Penn St. 27, No. 1 Georgia 23 (Sugar)
Jan. 01, 1979 - No. 2 Alabama 14, No. 1 Penn St. 7 (Sugar)
Jan. 01, 1972 - No. 1 Nebraska 38, No. 2 Alabama 6 (Orange)
Jan. 01, 1969 - No. 1 Ohio State 27, No. 2 Southern California 16 (Rose)
Jan. 01, 1964 - No. 1 Texas 28, No. 2 Navy 6 (Cotton)
Jan. 01, 1963 - No. 1 Southern California 42, No. 2 Wisconsin 37 (Rose)
Note - there have been a few games between BCS #1 and BCS #2 teams that did not own the top two spots in the AP poll when they played.
In 2000 and 2001, Oklahoma and Nebraska met when they were #1 and #2 in the BCS (both times after the first week of the BCS rankings). They were #1 and #3 in the AP in 2000 (#3 Oklahoma won), and #2 and #3 (#3 Nebraska won) in the AP in 2001. Also, the BCS title games after the 2000, 2001, and 2003 seasons featured games between teams that were not 1-2 in the AP poll. After the 2000 season, AP #1 Oklahoma defeated AP #3 Florida State; after the 2001 season, AP #1 Miami defeated AP #4 Nebraska; and after the 2003 season, AP #2 LSU defeated AP #3 Oklahoma.