Rarest pokemon I ever caught was a Shiny Suicune. I was going to go get a mewtwo and walked in some grass accidentally and the music played and I was like "YES SUICUNE!" then I saw it was a differnt color so I was like "OMG ITS SHINY!" and threw my masterball and caught it.
Depends on what you mean by "rare". Like shinies or One-per-game Pokemon. I've hatched a shiny ghastly, got a Jirachi from Pokemon Channel, and caught latios and latias + all the once-per-game Pokemon.