While not free, Populous: The Beginning on GOG is the most reliable version for modern Windows. It’s often on sale for under $2 and includes the Undiscovered Worlds expansion.
The Shaman’s AI can sometimes break on fast processors; the Populous: Reincarnated community provides patches to stabilize the game's logic. Why It’s Still Worth Playing Populous: The Beginning Free Download
This is the heart of the modern community. The Populous: Reincarnated Matchmaker provides a free client that allows for multiplayer gaming, high-resolution patches, and community-made maps. It typically requires you to own the base game files, but it is the essential "hub" for fans. While not free, Populous: The Beginning on GOG