I sometimes save where ever I am, but in white I have this thing about going to Nimbasa City and saving in front of the Ferris Wheel. I don't know why, but I almost always do if I'm not in the middle of something important and can fly there.
OMG, I love having a "home"... but I call it a "home base". I started having one in HeartGold, saving my game a lot in Violet City (not hard to see why ). Now, in Pokemon Black, I've found a new Flying-type city that I use as my home base, Mistralton City. I love the planes!
I don't really save anywhere in particular, but if I had to choose a "home' it would be Undella Bay. The music is calm, it's near the beach (well it IS the beach), and my favorite pokemon resides there .