Ok, I'm gonna list each canon Metal Gear game here, the system(s) that they're on, and the year that it takes place.
Metal Gear for MSX (1987) and NES (1988 )-- original game, 1995. MSX version is better, although the NES version is the only one you can find in NA
Metal Gear 2: Solid Snake for MSX (1990)-- sequel, 1999. Never left Japan; NA got a game on the NES that was Metal Gear in name only.
Metal Gear Solid for PS1 (1998 ) and Metal Gear Solid: The Twin Snakes for GC (2004)-- 2005. Same story in each, though Twin Snakes had a graphical, sound, and gameplay makeover. Both games have text recaps of Metal Gear and Metal Gear 2: Solid Snake, so there's no reason to play the older games before this unless if you just want to play through the entire series in order (see the MGS3 entry later on how to do that). I personally enjoy Twin Snakes better than the original (gameplay has aged better), but it's mainly a matter of preference and console availability.
Metal Gear Solid 2: Sons of Liberty for PS2 (2001) and Metal Gear Solid 2: Substance for Xbox and PS2 (2002/3)-- 2007 and 2009. Think of Sons of Liberty as the theatrical release, while Substance is like the DVD release complete with bonus features and extras. It adds only one cutscene to the game, and I believe lets you find a silencer that wasn't in the original.
Metal Gear Solid 3: Snake Eater for PS2 (2004) and Metal Gear Solid 3: Subsistence for PS2 (2006)-- 1964. Prequel to the series (but they should be played in the order that they were released), Subsistence enhanced the original game by adding new camera controls, thus there is no reason to play Snake Eater. Also, Subsistence has a lot of extras, similar to Substance for MGS2, but it also has fully playable versions of the MSX versions of Metal Gear and Metal Gear 2: Solid Snake
Metal Gear Solid: Portable Ops for PSP (2006)-- 1970. Continues the story of MGS3 and acts as a "bridge" to the rest of the series.
Metal Gear Solid 4: Guns of the Patriots for PS3 (2008 )-- 2014. Meant to bring the entire series full-circle and end every story arc to date. Characters from each game to date are supposed to show up.
So that's the order that the games should be played, and bear in mind that the upcoming Metal Gear Essentials is Metal Gear Solid (PS1), Metal Gear Solid 2: Substance (PS2), and Metal Gear Solid 3: Subsistence (PS2). That has all 5 of the main Metal Gear games on it, excluding Portable Ops of course.
Non-canonical Metal Gear games include Snake's Revenge, Metal Gear Solid (or Ghost Babel) for Game Boy Color, Metal Gear Ac!d 1 and 2 for PSP, and Metal Gear Solid: Portable Ops + for PSP (which is mostly a multiplayer expansion pack for Portable Ops). These games are not part of the storyline, so you don't have to play them to understand the series.
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