While it's not rare at all, I have a lot of affection for the Super Mario Bros./Duck Hunt cart that came with my NES back in the 80's, if just because it was the first video game that was legitimately mine and mine alone, and I still have it to this day. (Along with the manual, at least.)
As for other things.. ...Hmm, I'm the sort that tends to have a lot of prizes that I'd never ever let go of, especially SNES RPGs, although extremely few of them have manuals even.
But a few notables..
Chrono Trigger and FF6: I've told the story before in another thread, about how I only got into these games a bit after they came out, so I had to get them used. By sheer luck they both showed up at a game shop at the same time soon after I started looking for them, and I traded in a few NES and SNES games to afford them(which I still regret, but I'm re-buying them still at least).
Tragically they only came with copy machine manuals, but both for being great games and the sacrifices I made to get them, I value these carts greatly.
Super Robot Wars: Original Generations 1 & 2(GBA), complete with everything. I lucked out and found both of them new at EB while looking for something else, and snapped them both up instantly. SRW stuff coming out overseas is pretty rare, and they didn't get a massive run.
Suikoden 2, complete. I got it as a birthday present from someone who didn't know much about video games back when it came out, and I hadn't even heard about the series at the time. I lucked out because not only did this game get really expensive later on, but if not for getting it I would have missed out on a really fine game series as well.