When I learned how to clone. Oh how I whored that glitch like a bitch.
The runner dogs aren't much of a problem when you have 10+ Master Balls.
Also my shinies are of course memorable. I got a Shiny Cleffa from the egg you get from the day care couple in Crystal, I got a shiny Paras from the Ilex Forest (unfortunately, I had already caught one and taught it fury cutter. =( so that sucked) a shiny Krabby, and a shiny Larvitar I got when I was hatching an egg for a friend. I cloned it of course.
Unfortunately, all of those are lost due to me starting new games in spite of the shinies.
But I've played through the game dozens of times, often making theme runthroughs, like mono type and stuff. A few times I traded over rare eggs of things like Snorlax and Larvitar to a new file from my friend's Gold version, so I could start over on my Crystal with a powerful team at the beginning.
But uh, as far as story goes, the SS Aqua was the best. Goin to Kanto and shit, it was pretty awesome. I was pretty disappointed Mewtwo's cave was gone though.