Definitely. I really hate the generic cases gamestop has and will not buy it unless it's a last resort or under $3. and even then I pull them out and toss 'em :lol
Although I do like the weight the manual gives, and you could always print out a cover. Although, what are the odds of getting a case with a manual but no cover art. :-X
For me I think it's 'cause carts can take more damage, they usually came in a cardboard box anyway so chances are the box would get wrecked before the game would. Only cardboard case I still have is my Double Dragon Advance game and I only got that like last year.
As for discs, they're discs. They're pretty fragile and without the case and manual, it just doesn't feel like a game to me
I generally prefer to get games in as good of condition as is possible including package and instructions. If I ever choose to sell said game, it will hold more value that way.
I prefer to get used games with the original box and the manual, but usually only on the newer gen systems. On NES, SNES, N64 stuff I don't care as much.
I'm a collector, so it definitely matters to me. If I can't find a copy with the original box and manual, I'll settle for just the game, but I'll still continue my search to see if I can find one complete.