Ah Body Slam vs Thunder Wave. I've pondered this problem so many times. Generally, the things that Thunder Wave can't paralyze can threaten Jirachi out (Landorus[-T], Gliscor, Garchomp), so you wouldn't want to stay in and Body Slam them anyway. However, that's on paper. In an actual battle, Body Slam can be a lifesaver. These things can also switch into Jirachi as well, so that's a good opportunity to paralyze said ground types. Similarly, if you're forced to Body Slam in a certain scenario, like stopping a Rock Polish Landorus as it sets up, it can be millions of times better than Thunder Wave. Oh and Thunder Wave is just asking ground types to come in once they see your set. Garchomp, Landorus, Gliscor, Dugtrio, Mamoswine, and bulky grounds like Hippowdown, Gastrodon, and Donphan (that's every ground type in OU, by the way), can all come in on the Thunder Wave set extremely easily and without risk. However, of course, Body Slam is inconsistent and only paralyzes 60% of the time. Fun Fact: There's a 4.6% chance that you paralyze all 6 of your opponent's Pokemon with only 6 Body Slams. If your team depends on paralyzation, I'd probably go with Thunder Wave.
Actually, this makes me think about SDefRainRachi with Thunder. It has the negatives of both Thunder Wave (can't hit grounds) AND Body Slam (inconsistent) all to deal damage. Body Slam is less powerful, but it still hits grounds that can generally come in for free on SDefRainRachi. Why exactly should Thunder be used? It hits Tentacruel, Gyarados, Tornadus-T, Skarmory (thanks Baka Ki Eru Dogura for reminding me) and other bulky waters I suppose; but it still has both negatives. It also loses its 100% accuracy if Rain isn't up, which is even more inconsistent. Jirachi is also forced to use a -Spe nature so Thunder and Iron Head don't lose power. Is the damage output enough to justify using Thunder (on Defensive Jirachi)?