It's a tough call. On the one hand, anything Gen 5 (N64, PS1, ect.) or older, I don't care for the box, and while a manual would be nice, I know it's hard to come by. But anything that came in a DVD case needs to be complete. DS/3DS games are the same. I won't buy them unless they have the case and manual.
As for the games themselves, one the one hand, I buy games I intend to play. On the other, I have 2 PS2 games, 1 Game Gear game, and intend to get 2 PSP games, and an N64 game (and maybe a repro Genesis game), despite not owning any of those consoles, simply for collection's sake. Hell, I had 6 NES games before I ever got my NES. But those I consider special circumstances. I think of myself as a video game player, and a Mega Man collector.