It's interesting to look at it at different windows.
At the close of the 1989-90 season, Duke was the 6th winningest program of all time(IU was 12th) and had been to 8 Final Fours and 4 NCAA Finals. (4 FF's/2 title games under K, 4 FF's/2 title games under two other coaches) (at that time IU only had six FF's all time total but they had won an impressive five times in six trips. They now have 8 FF's) Duke was the #1 Bridesmaid at that time. Just could not win the big one, I'm sure they had the distinction of "Best program without an NCAA Championship."
Fast forward 25 years and Duke is no longer 0-8 in FF's, they've won it 5 times in 8 more trips to the promised land and moved up two more spots on the all-time victory list from 6th to 4th and are one of only four schools with 2,000+ wins.
I felt with the combo of wins and FF'S and 4 titles prior to 2015 that they moved ahead of IU anyhow but for those who lean strongly to NCAA Titles, that gap is now shut with IU and Duke. And Kansas now trails by 2 National Championships.
Updated stats through 2014-2015:
Most NCAA Championships:
1. UCLA-11
2. Kentucky-8
3. Duke/IU/UNC - 5
4. UCONN-4
5. Kansas/Louisville-3
6. lots of teams with 2.
Most NCAA Championship game appearances:
1.Kentucky/UCLA-12
2. Duke-11
3. UNC/Kansas-9
4.Indiana-6
5. Ohio State -5
6. UCONN/Georgetown/Michigan-4
Most Final Fours All-time:
1. UNC-18
2. Kentucky/UCLA -17
3. Duke-16
4. Kansas-14
5. Louisville/Ohio State-10
6. Michigan State-9
7. Indiana-8
8. Arkansas/Cincinnati/Oklahoma State-6
9. Stopping here, as seven teams have 5 Final Fours (UCONN, Florida, etc)
Most Final Four wins:
1. UCLA-25
2. Kentucky-21
3. Duke-17
4. UNC-15
5. Indiana/Kansas-12
6. Ohio State/UCONN-8
7. Cincinnati/Louisville-7
Most NCAA Tournament wins:
1.Kentucky -118
2. UNC -112
3. Duke-105
4. UCLA-99
5. Kansas-97
6. Louisville-75
7. Indiana-64
8.Michigan State-63
9. Syracuse-61
10. UCONN-56
Can someone post the all time wins list for the top 10 that includes the 2015 season?