Sipho is described as 'action survival game with an intricate building system. Grow your own creature and take over the local ecosystem. Fight, grow, survive, dominate'. There are four alternatives to Sipho for a variety of platforms, including Mac, Windows, Linux, Steam and Online / Web-based. The best alternative is Spore. It's not free, so if you're looking for a free alternative, you could try Captain Forever. Other great apps like Sipho are Captain Forever Remix (Paid) and Reassembly (Paid).
Described as "Meccano Asteroids", Captain Forever lets you pilot your own modular spacecraft, while simultaneously constructing it. Captain Forever is a collection of browser based games that run in Flash. You can play the first game free right now.