Copycat and Magnet Train Rail Pass
To get the rail pass for the Magnet Train in Saffron City, first go to a two-story house on the northwest side of Saffron City. Go to the second floor and meet Copycat, a girl who mimics other people. She will tell you that she lost her Clefairy doll in Vermillion City.
Return to Vermillion City and visit the Pokemon fan club. Speak to the man to the left of the Chairman of the club, and he will provide you with the missing Clefairy doll.
Return to Copycat's house and give her the Clefairy doll. In return, she will give you the Magnet Train Rail pass, which will allow you to travel from Saffron City in Kanto to Goldenrod City in Johto.
Mr. Pokemon and the Exp. Share (In Exchange for Red Scale)
Travel back to Cherrygrove City and go north to Route 30 and Mr. Pokemon's house. He will ask you where you found the Red Scale*, and he'll offer to trade you the Exp. Share for it.
*The Red Scale is obtained after battling the shiny red Gyarados in the Lake of Rage*