What is unique about the Metal Gear Solid series is you can't expect what will happen next in the game, Hideo Kojima knows how to surprise his fans by delivering unexpected story twists and hidden secrets.
Beware!! this article contains a lot of spoilers, so if you haven't played all of the Metal Gear Solid games don't continue reading.
Every game in the series have a lot of surprises, but these what comes to my mind when I think about the series as a whole. You may agree or disagree with my list, so feel free to list your WTF moments in the comment section below.
5. You can find the frequency for Meryl codec (140.15) on the back of the CD!!
When you finish battling with Ocelot in MGS 1, Baker advises Solid Snake to contact Meryl via codec, and guess what? you can't find her codec frequency any where in the game, you can find it only on the back of MGS CD.
This is one of the many examples how Kojima tried to make a Physical connection between the player and the game. This trick made me laugh at my self because I didn't catch what Kojima tried to do at that time.

4. Psycho Mantis can read your memory card!!!!
Psycho Mantis is one of the best villains ever created in videogames. He is a freak who can read peoples minds, and when he tried to read Solid Snake mind in MGS he do it with a little help from your memory card. If you have played Castlevania: Symphony of the Night and saved your progress in the game, he will tell you that you are a fan of Castlevania.
In the Gamecube (MGS:Twin Snake) and Playstation versions of the game you need to switch your controller port back and forth to prevent him from reading your mind, so you can hit him with your weapon.
Also he can move you controller, check the video below.

3. You can kill The End by forwarding your Playstation 2 Clock!!!!!
The End is a member of the Cobra unit with an exceptional sniping skills, so if you don't want to struggle with him you can simply turn off the console and wait for seven days (if you are a patient man) or set the system clock a week ahead.
The first time I faced The End it took me more than one hour, he is very good with hiding. So when I discovered that you can kill him by setting the system clock a week ahead. I was surprised, then I was amazed by Kojima.

2. Solid Snake isn't the main character in MGS2!!!!!!
Kojima released all the trailers for MGS2 featuring Solid Snake as the only playable character in the game, as all of you know by now this is not the true story at all.
Snake sneaks down to the hold in order to record pictures of the new Metal Gear (Ray), Matters rapidly escalate as Revolver Ocelot betrays and murders Sergei Gurlukovich. After that an unexpected scenario will happen, you will play as Raiden who will became the main character in the game.
At the beginning of the plant chapter Roy Campbell briefs someone about his objectives and explain why he was sent to the big shell, during that cut scene I heard a different tone of voice from what I used to hear from solid snake, I thought may be because of playing the game too late in night and i was very sleepy there is something wrong with my ears. After he take off his mask, I said to my self "what is this...where is the fuck is solid snake?"

1. Big Boss is alive!!!!!!!!!!!!!!!!!!!!
After you think that you have finished MGS4 and Old Snake has shot himself, the game credit starts rolling and rolling until a name is displayed, and this name is no other than the legendary soldier Big Boss.
"Good. That's right. No need for you to go just yet. It's been a long time....Snake" that what Bigg Boss said to Solid Snake, and I was saying to my brother who watched me playing the game from the beginning " What !!  Big Boss is still alive ? What the fuck is going on?" even Solid Snake said " How can you still be alive?".
It was a very memorable moment in my life as a gamer and it's definitely one of the best moments in gaming history.