Yellow- Looking back...I've never beaten an original game from that generation (E4 counts as beaten)! >_< I need to finish Yellow before the battery dies, just to say I have...
Gold- Too long ago to remember. =P It was most likely the level 70 Lugia, or it could've been one of the three gerbils. My bet goes with one of those two.
Ruby- It's been a variety of things. First two runthroughs, I didn't even finish the E4 either (pattern, anyone? =P), so I think I either saved it or used it on a Groudon. My third playthrough, which I recently deleted with exactly 230 hours, I used it on whichever Lati is in Ruby, partially because they're annoying and partially because I killed Groudon. I think it had something to do with it taking over an hour, perhaps because of explosion...
Sapphire- I used it on a Kyogre, since it was my brother's, and I knew he wanted it back really soon, so I just wanted to beat the 8 gym leaders and then he could have it, since I already had the data from the other Lati from one of my friends who has Emerald.
Fire Red- The fight with Mewtwo. The next fight was Entei, who promptly roared and ran away forever. *sob*
Pearl- First playthrough, I made it to like the third gym and just got bored with the game. Second and current playthrough, I used it on a Palkia. I had literally one pokemon left at medium health after the fight, and it was 7 levels below him, so I just kinda gave up and threw it away, not wanting to go through that fight again. Having seen the running Spirit at least 3 times now, I kinda wish I had kept it...oh well.
I've already started my Ruby over, and I'm starting over my Fire Red as well as soon as I finish uploading the Pokemon...why NIntendo needed to add that stupid 6-a-day rule, I'm not sure. I'll probably use it on the Lati again for Ruby and save it for the gerbil on Fire Red.