You give it to Charlie Brown when he has to sign the contract in the football scene with Lucy. Get the pen when you give Linus the sucker from Pigpen -- it is on his desk.
Between getting the pen and using it, there are two sequences :
1) Snoopy blowing leaves and Linus jumping into them
2) Linus going to mail his letter (you have to go back for his blanket in the leaves)
For Charlie Brown to sign the declaration that says that Lucy will not take the football away from him so that Charlie Brown can actually kick it (which is of course fake). So he signs it. Then he gets ready and tries to kick it, but Lucy takes it away. After that you get the football and throw it at Snoopy's hat, which is stuck in a tree.
You get it from Linus by giving him the sucker.
When you give him the lemon sucker from Pigpen. He gives you his invitation to the party, and you can get his pen from the desk.
It is on the table after you give Linus the lemon sucker from Pigpen. Linus gives you his invitation to the Halloween Party, and he has just written a letter to the Great Pumpkin. Pick up the pen.
There is no pigeon on great pumpkin island.
you go to Linus's house and get the pen off his desk
The pumpkin patch is to the right on Great Pumpkin Island. It was the only area shown in the island preview.
You can find the pen after you give Linus's candy bag to Pigpen, who is on the street. In return, he will give you a lemon-flavored sucker. Then go back into the house and give it to Linus, who gives you his party invitation. Pick up the pen, which he was using to write a letter to the Great Pumpkin.
You sign a contract.
The pen, which you need to do the Charlie Brown football scene, is on Linus's desk in Linus and Lucy's house. It will appear when Linus is writing his letter to the Great Pumpkin. This is after you have selected the pumpkin in the pumpkin patch and rolled it back to the house. Take the bag that Linus gives you and give it to Pigpen on the sidewalk outside. He will give you a lemon sucker. When you take this back inside and give it to Linus, he gives you his invitation to the Halloween party, and the pen is on his desk. Linus is writing a letter to the Great Pumpkin.
There are no buildings or upper rooms on Great Pumpkin Island.
After you get the invitation and the pen, Charlie Brown and Snoopy are in his backyard, on the far left of the island. You will play a mini-game as Snoopy gathers some leaves in a very relaxed manner.
The name of the island is Great Pumpkin Island. See the related question below.