A quick "JJ rundown" by series number:
2 - When the team works a case in New Orleans, JJ meets New Orleans detective William LaMontagne. They are mutually attracted and begin a long-distance relationship.
3 (near the end) - JJ discovers she is pregnant with Will's child.
4 (middle) - JJ has the baby and goes on maternity leave. For several episodes, she is replaced as media liaison by Agent Jordan Todd. Later in the series, JJ returns to the team and Todd leaves. (In real life, JJ's actress A.J. Cook had a baby, and JJ's absence was timed to accomodate Cook's maternity leave.)
5 - JJ is with the team for the entire series (and Will is shown as having moved to D.C. to be with her and their child), but there are some behind-the-scenes rumblings that she is being pressured to take a position elsewhere.
6 - JJ leaves the team for a position in the State Department (she is basically forced to), but makes a few guest appearances (she is listed as a recurring character for almost all of series 6).
7 - JJ returns to the team full-time, along with Prentiss, who left midway through series 6. Prentiss's story is a completely different can of worms!