Went it first came out I hated source, I was an avid 1.6 player and was a ringer for some cal teams briefly.  Something about the aiming and physics threw my game off, but I liked the new graphics and maps enough that I kept playing source and now I suck at 1.6...figures

besides the physics and graphics, a huge difference is the type of games and maps you will find in the two games.  1.6 had waaaay cooler custom maps in my opinion.
Maps with full amusement parks complete with giant rideable roller-coasters, knife maps with lots of drive-able vehicles, and DE_WALLMART was my all time favorite.  No one makes maps like that for source, maybe because they are harder to design, idk.