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[Marker Magikoopa]

There are some more two cows jokes at http://uncyclopedia.org/wiki/You_have_two_cows/24.
WARNING! Site may have some bad language. So I'm going to copy some of the Mario ones and post them here for the little ones who aren't allowed to use the above URL.

Paper Mario
You have two cows. One of them gets kidnapped, while the other one lands in a forest after falling from a castle that's floating in space, yet survives.

Paper Mario: Thousand Year Door
You have two cows. One of them hunts for treasure, while the other hunts for the first cow.

Paper Mario: Thousand Year Door (2)
You have two cows. Both turn into paper airplanes and float gracefully to the other side of the screen.

Any Mario game
You have two cows. You stomp on both of them without hitting the ground and gain 100 and 200 points.

Super Mario Bros.
Your two cows are in another castle.

Super Mario Bros. 2
You have a cow and a goat. The cow is released in Japan. The goat gets redone to look like a cow and is released in North America.

Super Mario Bros. 3
You have two cows. You hit the block that they are on and steal their giant shoes.

Super Mario World
You have one green cow with a really long tongue.

Super Mario World 2: Yoshi's Island
You are one green cow with a really long tongue.

Super Mario 64
You have two cows. You run circles around one of them until coins pop out of it.

Super Mario 64 (2)
You have two cows, but they are both trapped in the walls of the castle.

Super Mario 64 (3)
You have two cows. One of them has stolen your hat and revealed why you never take it off. Ever.

Super Mario Sunshine
You have two cow-shaped piles of goop. You spray them with water and they dissolve. Milk Get!

Super Mario Sunshine (2)
You have two cows, but that won't help you bring back the sunlight.

New Super Mario Bros.
You have two cows. One of them is a well-established cow who gets skeletonized by some lava even though it has survived lava before. The other one is some poser cow that is made the main villain for some reason.

Mario Kart DS
You have two go-cows. One of them snakes his way to victory and wins. The other one Disconnects.

Mario Kart Double Dash!
You have two cows. One is trying to drive while the other just presses 'L and R' to throw you off course.

Mario Kart 64
You have two cows. Both of them jumped while driving on the massive hill on Rainbow Road and overshot the actual "road" bit.

Super Mario Bros.
You have two cows. One of them comes out of a brick, makes you get bigger and shoot fireballs out of your mouth. The other one is in another house.

Super Mario Bros. 2
You have four cows now, but only two of them are useful. One of which is the cow you rescued from the first game. They can now stand on top of other cows and pick them up/toss them, but it is useless since all the cows involved suck. Your cows can level up, but if they ever get a game over, all their levels decrease. Also, the cows freeze up randomly during the last level.

Super Mario Bros. 3
Your cows are now much bigger and funner, with 8 world maps to explore. Your cows can also now turn into raccoons, frogs, and bears. All these powers are useless though, since you can skip 7/8 of these world maps and finish the game in 15 minutes if you are leet.

Super Smash Bros. Melee
Choose between 2 cows and get ready for an All-Cow bash!

Super Smash Bros. Melee (2)
You have two cows. They repeatedly thrash each other for no apparent reason until a giant white-gloved hand appears out of nowhere and deals with both of them swiftly and ruthlessly. You now have no cows.

Super Smash Bros. Melee (3)
You have two cows. One of them is a pfargtling cheater and used the homerun bat the WHOLE TIME. Now you have one cow.

Yes, I did censor the last one.

[vg]

Pikmin

You have 2 cows based on familiar characters. One gets lost and you have to find him. Truth is, he tried to kill you.

[Cherry]

[Super Maiq the Liar]

You had two cows, M'Aiq ate two steaks.

[Ruki Motomiya]

Keane:

You have two cows, but their in a place only they know.

[Legendary Mashine]

[Super Maiq the Liar]

UWAH! M'Aiq hopes to never meet those bulls in a dark alley...

[Nastasia]

Pokemon
There are two cows...
Wild Cow appeared!
Go Cow!
Cow used Stomp!
Wild Cow was defeated!

...I dunno xD

[Cherry]

Actually, it would go like this:

Wild Cow appeared!
Go, Cow!
Awesome used a Master Ball!
Wild Cow captured!

You now have two cows!

[Agent of Crime]

GameFAQs:

You have two cows. The cows have a violent disagreement over whether or not Toad will be in the next Super Smash Brothers game.

Evil Dead:

You have two cows. Ancient Sumerian demons possess your hand and you have to sever it. You replace it with one of your cows.

[Legendary Mashine]

Di Gi Charat -

You have a cow nyo! The cow is a great princess of a faraway planet nyo!
No, nyu! You have two cows, nyu! One of them is Puchiko nyu!
GEEEMAAAAA! YOU HAVE THREE COWS GEMA!!!
You have four cows! This cow is Rabi en-- *something large falls on the fourth cow*
Farewell, three cows. Farewell.


Excel Saga -

HAAAAAIIIIIIIIL TWO COWS!!!!!!!!!!

[Agent of Crime]

4chan:

u have two cowz omg lolz. u have two cowz omg lolz. u have two cowz omg lolz. u hav 2 cowz omg lolz. For repeating the same tired joke four times, your cows obtain internet fame.

[Ruki Motomiya]

Dragonball:

OOOOOOOOOOVER OOOOOOOOOOOOONE COOOOOOOOOOOOOOW!

[Marker Magikoopa]

A few others from Uncyclopedia.

Pastafarianism
You have two cows that can fly and are made of spaghetti. You insist that the Kansas School Board teach, alongside Intelligent Design and Evolution, the theory that your two cows created the universe. You dress like a pirate.

Pastafarianism #2
You and your two cows are dressed in full pirate regalia.

Pastafarianism #3
You have two cows. You worship them ironically because cow meat comprises the Holy Balls of the Flying Spaghetti Monster. Somewhere in Kansas, a School Board member chokes on a hamburger.

Pastafarianism #4
You have two potential sources of meatballs. There is a midget.

Pastafarianism #5
You have two cows because the Flying Spaghetti Monster used his noodly appendage to make them.

Jedi
You have two cows.... "..Yes, I have two cows"

Jedi #2
"May These two cows be with you."

Jedi #3
You have two cows. You lift them off the ground while upside on Dagoba.

Jedi #4
These aren't the cow's you're looking for.

Jedi #5
"2 Cows...I am your Farmer." "MOOOO!"

Jedi #6
2 cows + lightsaber = lots of pfargtling BBQ beef

Wikism
You have two cows because the article says you have two cows.

Should I apologize for bringing religion into this topic?

[Ruki Motomiya]

Star Trek:

Live long and with two cows.