In the games
In Generation I and Generation III, the Sea Cottage is home to Bill. He was experimenting with his cellular teleportation device when he was accidentally turned into a Clefairy. After he is rescued, the player is rewarded with a ticket for the S.S. Anne.
In the anime
While the Sea Cottage does not appear in the anime, the lighthouse in Mystery at the Lighthouse fills the same purpose of the home of Bill.
In the Pokémon Special manga
The Sea Cottage debuts in the Red, Green & Blue chapter as Bill's home and where he makes all his inventions. Bill is transformed into a mutated Rattata when he was fixing one of his two Pokémon Transporter. The round doesn't show another machine inside, but it has an antenna in its roof.