From Wikipedia: For the "Big 3" sports (football, men's basketball, and baseball), head-to-head Mississippi State leads Mississippi 421–361–11.
I found the championship numbers below from 2010 and updated them to include our 2012 SEC Baseball Tourney win. I don't think either of us won any other SEC Overall or Tourney Championships from 2010-2012.
It's been 49 years since Ole Miss' last SEC Championship in football vs. 71 for ours. As time goes on, those two are beginning to look closer and closer together.
Want to count those glory years?
http://en.wikipedia.org/wiki/List_of_SEC_Conference_Champions
Since 1965, they've won FOUR SEC Championships, all in baseball, and we've won TEN (8 baseball, 2 in basketball).
Since 1959, they've won TEN (3 football, 7 baseball), and we've won FOURTEEN (8 baseball, 6 basketball).
Since 1941, they've won THIRTEEN (6 football, 7 baseball), and we've won SEVENTEEN (1 football, 10 baseball, 6 basketball).
If you want to add "minor sports" to the Big 3--Women's Basketball, M/W Tennis, M/W Golf, M/W Track&Field, W Soccer, W Volleyball, and M/W Cross Country, then:
Overall SEC Championships since 1941: Ole Miss has won TWENTY (6 football, 7 baseball, 1 women's basketball, 5 men's tennis, 1 men's golf), and Mississippi State has won TWENTY EIGHT (1 football, 10 baseball, 6 basketball, 3 men's tennis, 2 men's golf, 1 men's outdoor track, 5 men's cross country).
**********************************
Overall SEC Championships:
Big3 sports, last 30 years: MSU 6,UM 1
Big3 sports, since 1965: MSU 10, UM 4
Big3 sports, all time: MSU 17, UM 13
All sports, all time: MSU 28, UM 20
SEC Overall and SEC Tournament Championships:
Big3 sports, last 30 years: MSU 15 OM 3
Big3 sports, since 1965: MSU 19 OM 7
Big3 sports, all time: MSU 26 OM 16
All Sports, all time: MSU 44 OM 25