To reduce your risk of getting banned on servers that allow or loosely monitor clicking:

He hopped back into the game, positioned his crosshair over the cobblestone generator, and took a deep breath. He tapped the activation key—

Instead of a separate program, many Eaglercraft players use custom clients that have auto-clickers built into the game's GUI. Popular options tested for performance and fairness include: Resent Client Shadow Client Astra Client

For advanced users, AutoHotkey offers customizable macros.