Randomly I've encountered Spinda in Ruby (lost... I've no idea where it went), Bellsprout in SoulSilver, Yanma and Garbodor in X (from horde and Friend S'afari)
About 100 of those were caught with Pokeradar in 4th gen and then I kept each stage separately, so it's not that impressive. Like I got a bunch of Eevees so I could get all Eeveelutions.
I also have softreseted 6 starters (Squirtle, Mudkip, Treecko and Johto starters), all the normal available legendaries in 3rd gen, some in 4th gen (Palkia, Giratina, Darkrai, Azelf, Uxie)
And random encouters. From which I'm mostly proud of my first Yanma from Black. It took me ages and I got most other shinies from route 14 before it finally appeared.
Then they made them a lot easier to get in 6th gen. Hunting in Friend Safaris, from horde encounters and chain fishing has been very productive, but I can't feel that strongly about them anymore.
Oh, and of course the legendary portals in ORAS were nice. Allowed me to get Kyurem, Ho-oh and Lugia a lot easier. And of course Zekrom and Reshiram, which were unavailable before.