Football - I love Front Office Football. It's a little dated, but it's the best and deepest simulation I have run across. It also has a sister game called FOF-The College Years. I am currently playing Gridiron and it's fun, but if you want realism versus the NFL you will be disappointed as the GE is not set up to deliver that kind of experience.
Baseball - Without a doubt it's OOTP for its depth.
Basketball - Don't have much experience outside of Buzzerbeater so it wins for now.