Atari 2600 6-Switch and 4-Switch vs. Jr.
Apparently many 2600Jr.s have a buggy TIA chip that causes Kool-Aid Man to be unplayable. It is possible that it may affect other games, but Kool-Aid Man is confirmed. See here :
Unlike all 6-switchers and many 4-switchers, the chips in the Jr. are socketed and not easily replaceable.
Some Atari 2600jr. have a single chip instead of the three chips of most Jr.s and all other 2600. They have video issues with the Harmony Cart's menu, and Kool-Aid Man and some interesting graphical anomalies with Pitfall II : http://atariage.com/forums/topic/196368-unicorn-boards-and-harmony-cart-menus-single-chip-2600-compatibility/
As far as the 6-switch vs. the 4-switch models go, the 6-switches (and the Jr.) have a video buffer chip that provides better video quality than the 4-switch. Some cartridges or controllers may find it easier to fit in a 4-switch or a Jr. than the Light or especially a Heavy Sixer.
Atari 5200 4-Port vs. 2-Port
Not much of a comparison here, the ability to play four player games on the 4-port 5200 is balanced against the ability to use the VCS Cartridge Adapter to play 2600 games on the 2-port 5200. However, the 4-port 5200 can be modded with eight passive components to provide the required compatibility. See Here : http://www.atarimuseum.com/videogames/consoles/5200/cx55.html
In addition, the 4-port 5200 uses a combination RF and power switchbox that is known for its fragility. The 2-port uses a simple power adapter and separate RF output. Fortunately, it is not too difficult to mod a 4-port for separate power and AV output.
NES - Front Loader vs. Top Loader
The Front Loader may have issues with its connector, but typically a good cleaning of the connector and carts a visual inspection of the pins can solve virtually any problem. The Front Loader has AV out, which the Top Loader lacks. Top Loaders are RF only. In addition, the output on a Top Loader is crap. A fix like this : http://www.stoneagegamer.com/nes-toploader-av.html would will restore the video quality, but you have to drill holes in your system's case or remove the RF unit. Not a beginner's mod.
Also, Game Genies don't fit properly in a Top Loader. There was an official adapter made for the Game Genie, but it is extremely rare. You could use a NES PowerPak or Everdrive N8, which support five Game Genie Codes as opposed to the three codes of the real Game Genie. Finally, there is no power LED on a Top Loader.
Sega Master System Model 1 vs. Model 2
Compared to the Model 2, Sega Master System Model 1s have a card slot in addition to the cartridge slot. The card slot let you play those games that shipped on a Sega Card. It also is required for the Sega 3-D Glasses. They also have an Expansion Port, which was unused officially but can be used for an FM Chip mod. They have a port with composite video and RGB connections on the back whereas the Model 2 is RF only. You can officially only play the Snail Maze game on early Model 1s, and the Model 2s lack the Opening Logo and Tune on startup. There is no power LED or reset switch on a Model 2.
Genesis - Model 1 vs. Successors
The Model 1 is the only system which works as designed with the Power Base Converter. While there are SMS adapters that fit in the Model 2, they do not offer a card slot.
Most Model 1s do not have the TMSS protection, which adds a second or two to the boot time of any game with the message Produced By or Under License from Sega Enterprises, LTD. At least five US games will not work with TMSS Genesis machines.
There are two motherboard revisions of the Model 1 with TMSS. One has the words HIGH DEFINITION GRAPHICS in white around the circle bordering the cartridge port. The second omits the words. All consoles with those words are considered to produce the best sound of all Sega Genesis models. The Model 1 without the text has much poorer sound. The Sega Genesis Model 2s have variable sound quality.
Model 1s have a headphone jack and use a power adapter with a plug that also fits into NESes, Famicoms and Sega Master Systems. Model 2s omit the headphone jack but have stereo audio on their AV ports.
Game Boy - Original vs. Successors
The original Game Boy is larger than the Pocket, Light or Color. It has larger buttons and a larger speaker and better quality audio. There are games like Castlevania II : Belmont's Revenge and The Legend of Zelda, Link's Awakening which rely on the properties of the green LCD screen found in the larger Game Boy for certain graphical effects. The Game Boy 4-player adapter does not require a converter. Batteries last much longer in it than the Pocket or the Light.
SNES - Original vs. 1-Chip & SNES Mini
Most of the original boxy SNESes use a separate CPU and a two-chip PPU solution. Late SNESes and all SNES Minis combine the CPU and both PPU chips into one large chip, called the 1-Chip. While the graphics are slightly sharper than on earlier SNES models, some games suffer from graphical inaccuracies on the 1-Chip models, some games with enhancement chips run slower, some colors combinations suffer from ghosting and the whites are overly bright. See here for more info : http://www.racketboy.com/forum/, go to forum called Guides under The Garage and look for the following thread, "SNES Console Revision Differences. SHVC-CPU-01 vs 1CHIP-Mini".
Playstation vs. PSOne
The PSOne is the slim version of the Playstation console. It has a different looking menu for CD-audio playing, and a port for a matching Sony LCD. But it looses the separate reset button, Serial and Parallel Ports, both of which have their uses, officially (serial for PlayStation Link Cable) or otherwise (parallel for Game Sharks). It is harder to install a mod chip in a PSOne due to the tighter space. There is an upcoming SD card solution for the Playstation called the PSIO which allows you to play CD backups from disc images, but it fits into the parallel port found on the SPCH-7xxx and lower, so no PSOne users need buy.