Which Creatures game is the best?
That depends. Each have their quirks, advantages, and shortcomings. The first were more charming, bigger, more "hands off", and show the sort of experimental and silly spirit common to early game developers (Easter Eggs, etc.). The later games, on the other hand, were far more polished and gamelike, and add neat new features and new levels of complexity lacking in the first.
In Creatures 1 (I can't speak for 2), the world was one long wrapping band (being a ringworld), which made it fun to explore: generations would pass as your Norns traveled from their hatchery out into the world, across or under the sea to distant islands, and so on. This also meant you had geographically isolated creatures evolving to be very different, with very different food sources and tools at their disposal. Also, you couldn't directly move your creatures around, which I think really added to the challenge and "hands off" gameplay style; in order to direct your Norns or explore the world, you had to get inventive and lure them with objects, or teach them language enough to direct them through words. The game definitely had more charm too, with the claymation-like world, the ramshackle hybrid of nature and machine, and the variety (and slightly campiness) of the Norn designs.
In Creatures 3 and its expansions, the Norns (and their rivals the Grendels and Ettins) their brains, their genetics, and so on were a lot more complex, as was the world itself; though smaller and quicker to explore, you had various biodomes, each containing several smaller ecosystems which you had to manage to supply food. You also had gadgets which you could assemble for a number of purposes; for example, I made a hovering sludge turret that detected Rival species in my Norn's preferred Biodome, approached them, and opened fire on them if no Norns were in the line of fire... all created with functional widgets, detectors, and logic gates. Other new features, such as item replicators, gene splicers, medical bays, chemical injectors, etc. added a lot more game options, depending on how involved you wanted to get in the world.
In either case, I'd strongly advocate the use of certain mods. Looking around, it seems that the Creatures community is still producing mods, tweaks, and new content over a decade later, and a lot of it looks to be pretty significant. In particular, the
Creatures Full of Edits tweak addresses some bugs, and improves the AI and organic modelling significantly.