Posted this a while back. You could make a decent argument for LSU or Ohio State as #2

Alabama
203-63 (76%)
5 National Championships
7 National Championship Appearances
5 Playoff Appearances
9-3 Record in National Championships and Semifinals
14 Top 25 Finishes
13 Top 10 Finishes
6 Conference Titles
17 Bowls (12-5 Record)
4 Major Bowl Appearances (1-3 record)
2 Heisman Winners
3 Losing Seasons

Clemson
195-70 (74%)
2 National Championships
4 National Championship appearances
5 Playoff Appearances
6-3 Record in National Championships and SemiFinals
14 Top 25 Finishes
6 Top 10 Finishes
6 Conference Titles
18 Bowl Appearances (10-8 records)
5 Major Bowl Appearances (3-2 record)
0 Heisman winners
1 Losing Season

Florida
181-76 (70%)
2 National Championships
2 National Championship Appearances
0 Playoff Appearances
2-0 Record in SemiFinals and National Championships
13 Top 25 Finishes
8 Top 10 Finishes
3 Conference Titles
18 Bowl Appearances (9-9 record)
7 Major Bowl appearances (4-3)
1 Heisman Winner
2 Losing seasons

LSU
202-59 (77%)
3 National Championships
4 National Championship Appearances
1 Playoff Appearances
4-1 Record in National Championships and SemiFinals
17 Top 25 Finishes
8 Top 10 Finishes
5 Conference Titles
20 Bowls (13-7 record)
9 Major Bowl Appearances (7-2 Record)
1 Heisman winner
0 Losing Seasons

Ohio State
217-43 (83%)
2 National Championships
4 National Championship Appearances
3 Playoff Appearances
4-4 Record in Semifinals and National Championships
17 Top 25 Finishes
15 Top 10 Finishes
9 Conference Titles
19 Bowls (11-8 Record)
10 Major Bowl Appearances (8-2 Record)
1 Losing Season
1 Heisman

Oklahoma
219-49 (81.7%)
1 National Championship
3 National Championship Appearances
4 Playoff Appearances
1-7 Record in National Championships and SemiFinals
18 Top 25 Finishes
15 Top 10 Finishes
12 Conference Titles
20 Bowl Appearances (9-11 Record)
8 Major Bowl Appearances (5-3 Record)
0 Losing Seasons
4 Heisman Winners

USC
188-71 (73%)
1 or 2 National Championships (Add the 2003 AP Title if you like)
2 National Championship Appearances
0 Playoff Appearances
1-1 Record in Semifinals and National Championships
14 Top 25 Finishes
9 Top 10 Finishes
7 Conference Championships
16 Bowl Appearances
7 Major Bowl Appearances (6-1 Record)
1 Losing Season
3 Heisman Winners