Yep, I try to give every single pokemon a name, though they aren't always so great. A lot have names with actual thought behind them, but the majority end up named after a random word or song that crossed my mind when they were caught/hatched. Sometimes the box pokemon will get theme names, but not too often. The pokemon on my teams are the lucky ones- they might receive names that were planned beforehand. For instance, in my Diamond team, Twoflower, DeForest, Geordi, and Skip were all pre-decided names, but Kermit, Freddy and Julio were spur of the moment names based on their personalities (or, the personality I saw while battling them).
And in Emerald, except for the starter who got a name themed to match the trainer (Swampert was Garfunkel and Brendan was Simon), my team all had names based on characters in the anime (Jessie, James, Brock, Megumi), but the FR team were all pretty much random. (Bar Onix, who was named after a fellow Brock girl~) Kojiro the Gloom was named 'cause he's blue, just like my favourite cucco, and the rest had names that were more or less the same inspiration-wise. The Yellow team's names weren't so great, though. :\
But I do like a lot of the names that the box pokemon have, and I might post some later.