I've kept them since the SNES though with the SNES I threw out the inserts that held the game and flattened the boxes. The sad part is most of the games I had the boxes for were stolen or never given back when I loaned them out. My N64 collection is all boxed. I'm glad modern games use hard plastic cases (Or Sega games since the SMS) that aren't as easily damaged and double as a case. I can see why people threw out their Gameboy & GBA boxes. Most of them were pretty ugly. The boxes for most games in Japan are much more attractive. Less focus on the name of the system and more focus on the art. American boxes tend to be tacky in comparison.
Buying used games I'm a bit of a perfectionist. I was collecting Gamecube games two years ago and I would make sure I was getting the case in good condition with manual. I was collecting all the RAREWARE games for the N64 and have most of them in box but won't buy the two or three I'm missing without the box + manual. Sadly I should have bought them all a number of years ago when they were still dirt cheap and often still brand new. Perfect Dark + Conker brand new sealed for under $14 for both was a good deal though.

