It seems to me like Nintendo Consoles are the most collected consoles in the hobby. I understand that Sega and Atari has less of a fan base because they are out of the industry, but why are Sony and Microsoft less collected for hen say N64 and GameCube?
The N64 and Gamecube were ignored by a huge majority of gamers when they were the current consoles on the market. Now people are looking back, seeing that there were some real gems on those consoles like the NES and SNES before them and are collecting for them. The prices are ballooning more for N64 and Gamecube I believe because with lower installed bases, these games had lower print runs than NES and SNES titles.
Nintendo consoles have huge nostalgia factor which contributes to their healthy aftermarket as well. Sega stuff is just out of favor and doesn't have the same draw (see the Genesis vs SNES thread). PlayStation has been picking up steam on the collector's market. Remember that the original PlayStation was released at the same time as the N64. Many PS1 RPG's and classics like Crash Bandicoot and Spyro the Dragon have risen steadily in price. Capcom titles are astronomically high priced. Atlus RPG's are commanding insane prices these days as are Working Designs games. PS2 games are beginning to creep up in price.
Xbox? While I think the original Xbox had a nice little library of fantastic exclusives, the system couldn't compete with the PS2. Most Xbox games are pretty cheap. Xbox 360 is just a failbox with fewer exclusives and forgettable games.