MGS3's an odd case because it's actually the first game chronologically (by the way, get Subsistence if you get MGS3. Good extras, the classic 2D Metal Gear games, and a better camera system). You play as the father of the main character from all of the other Metal Gear and Metal Gear Solid games, as this takes place in 1964, while the others take place from 1995-2009.
Think of it kinda like Star Wars. Most people who watch Star Wars watched episodes 4, 5, and 6 first, and while various things are mentioned or implied, you don't know the whole story until you see episodes 1, 2, and 3. You know that Anakin Skywalker becomes Darth Vader, you know that Obi-Wan Kenobi and Yoda are the only Jedi left, and that there's a Galactic Empire at the head of it all when you watch ep 4, 5, and 6, but you have to see 1, 2, and 3 to find out how that happened.
Same with Metal Gear and Metal Gear Solid (minor series spoilers here). Solid Snake is the main character of Metal Gear, Metal Gear 2, Metal Gear Solid, and the first part of Metal Gear Solid 2. From playing the first two games (which made in the 80's), you know that there's an American stealth commando unit called FOXHOUND, and that it's led by a man codenamed Big Boss. Big Boss is the father of Solid Snake, the main character, but he's also the final boss of the first two games. How did FOXHOUND come to be, why did this American hero (Big Boss) decide to point a nuke at his own country, and what's the deal with this guy named Ocelot who shows up in all of the Metal Gear Solid games? Also, how does a group discussed in MGS3 relate to a group in MGS2, a game which takes place 45 years later?
Metal Gear Solid 3 and Portable Ops (the PSP game) answer those questions. So essentially, it's up to you. Play the games in the order that they came out (Metal Gear Solid on PS1 or GC would be the place to start if you decide to do that... you can read the story of the old 2D games in MGS) or in chronological order. If you play MGS3 and Portable Ops first, you'll be starting at the beginning, but some twists in the later games will be spoiled (kinda like how if you watch Star Wars 4, 5, and 6 first, a key moment in 5 is pretty unexpected. If you watch 1, 2, and 3 first, you already know what's going to happen).
Anyway, here's the current timeline. Start where you will.
1964: Metal Gear Solid 3 (PS2)
1970: Metal Gear Solid: Portable Ops (PSP)
1995: Metal Gear (MSX, NES, and MGS3 Subsistence)
1999: Metal Gear 2: Solid Snake (MSX and MGS3 Subsistence)
2005: Metal Gear Solid (PS1) or its remake: Metal Gear Solid: The Twin Snakes (GC)
2007-2009: Metal Gear Solid 2 (PS2 and Xbox)
2014?: Metal Gear Solid 4 (PS3)
Whatever you decide, don't play MGS2 first. MGS gives you the backstory on the older games, and while MGS2 does that, it's a very long read, and it's supposed to be a suppliment to what you've already played in the previous game. Likewise, Portable Ops shouldn't be played w/o beating MGS3 first.
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