I own a handful of Nintendo games that I did not want to sell with the rest of my collection. They are either rarer titles or stuff I got while I was in Japan. Mostly unremarkable stuff, just nostalgic. Higurashi, some Gundam games, Pokemon, etc. Plus, I do have Mother 1&2, and Mother 3. Those are the pride of my Nintendoless Nintendo collection. I just know if I get back into Nintendo collecting I will regret selling those. Even if they are cheap, they were my copies from when I was in Japan.
I have been toying around with expanding my collection to portables. I take the train to work, which provides a good excuse to buy portable systems. If I do this, I will probably buy a few DS/3DS games before I buy a 3DS.