When I was younger I just tried catching every Pokemon that I saw and didn't already have, and let a majority of them just sit in the box for eternity.
Now that I don't really care about completing the Pokedex anymore, I'll only catch the Pokemon I know that I'm going to use for at least a little while, otherwise I just see it as wasting Poke Balls. Sure, there are some I'll get through different things like the GTS and the Safari Zone that I don't really plan on using, but those Pokemon are few and far between now compared to before. My last look at HeartGold for example, I had only 2 1/2 boxes full of Pokemon after hundreds of hours played, whereas on my original Sapphire I had to start releasing Pokemon because I had way too many in my PC (this led to me inadvertently finding that I had a shiny Shroomish in one of my boxes, though).