For me, the best moment is the two hour season finale. I could do without the whole Pleasantville alternative (Paige references Pleasantville which was funny but that actual alternate universe was not). The two hour was the best because of scenes with Leo and Chris and then with Leo and Paige when she tells him Chris is fading.
Adult Chris gets injured. And Chris and Leo get the scenes that you've waited for all along.
I also enjoyed alternate Paige and Phoebe (evil and dark). And Alyssa Milano really got to shine with little moments (that were probably her own and not scripted) that just made Phoebe and the family seem all the more real. (Like "Where did the baby go? Where did your brother go?" She asks Wyatt that when Leo takes baby Chris to see Piper.) I think it was Alyssa's best episode. She also looked the best she did all season. (She's always highly attractive and probably never has even a bad hair day but she really looked good in the two hour conclusion.)
Other than that, the second best would be Phoebe's high school reunion. Again, Alyssa really got to shine.
The best parts of the season revolved around family. At one point, Paige was creating a mythical lover for herself and that was probably summing up the whole season because Leo and Piper were split for most of the season and Phoebe and Piper really didn't fnd lasting love (not with Jason, not with Richard). Oh, I also really loved it when Piper had her dad come spend time with Adult Chris.
"Iraq snapshot" (The Common Ills):