The original Nintendo we all know and love was replaced by the "Dogbone" style. While smaller and sleeker, the top loader is also more reliable, and therefore sought out by collectors and retro game lovers.
The original SNES got a redesign just like the first, but the aspirations of the "Play Station" CD add-on and what could have been ended up birthing their greatest competitor.
The original Game Boy got smaller with the Pocket, and eventually went to color games. I think there was even a lighted version of the black-and-white out there somewhere.
Many great games came out that required you doing surgery on your system to insert the "Expansion Pak". While never released outside of Japan, the 64DD was clicked onto the bottom to add more gaming fun (with only nine total cartridges released for it, though.)
The Virtual Boy didn't get off the ground, but it had ports on the bottom, ready and willing for who knows what. Some may even say that the 3DS is a logical "upgrade" to the ideas behind this system anyways.
The terribly lit original was upgraded to the clamshell style SP, and at the end of the cycle was given a trendy redesign into the Micro.
Nintendo started to show ideas similar to the Wii U when it allowed you to tether your GBA to it, creating some unique and fun games. The bottom was chock full of ports and possibilities, mainly used for the 'net adapter and the GBA player.
The original DS got smaller, then larger again via the DSi and DSiXL (which for me wasn't significantly different, other than a scant few games and the downloadable section).
Wii's guts mainly changed, nixing the GameCube support for frustratingly mysterious reasons to a retro gamer. It went even further, hacking out online support in the rarely-seen Wii Mini. Wii controllers themselves deserve their own section in this list, as the WiiMotionPlus accessory (and later built in component) gave the Wii Remote the "what it should have been" upgrade it deserved.
The 3DS definitely got an upgrade via the 3DSXL. Many wondered why the Circle Pad Pro wasn't integrated into the system. Myself, I feel that adding that makes it look like it could one day sync up and be your second Wii U GamePad.
As you look back, you can really see Nintendo's thought progression. After all, Zapper + Power Glove + Power Pad = Wii Experience. The GBA SP stylings led to the DS Lite. Circle Pad Pro mimics what we see on the Wii U GamePad. Nintendo's always looking for a way to upgrade to version 2.0. Will we see that in the Wii U? Only time will tell.