This is a good question, though not one easily addressed with a simple answer.
As @Mat0 commented above, one difference is the approaches that the various platforms are using to achieve consensus. Some use proof of work (PoW), others use variants of byzantine fault tolerant strategies (PBFT, SBFT, etc). Some use PAXOS derivative strategies. Hyperledger Sawtooth Lake has developed an innovative strategy named Proof of Elapsed Time (PoET). Some, such as Hyperledger Fabric allow pluggable consensus implementations to allow for experimentation and additional diversity.
Other platforms differ in the means by which they implement confidentiality of data and transaction execution.
Some such as Hyperledger Fabric, Hyperledger Sawtooth Lake, Corda, Ethereum and many others permit more comprehensive smart contract capabilities, while other platforms are very restrictive of the types of contract operations - such as the various platforms that only support the limited set of operations in the unspent transaction output (UTXO) protocol.
Some are more targeted to a specific use case, while others are more intended to be more general purpose. All are seeking to find ways to improve the various aspects of performance and scale.
Finally, some are intended to support permission-less public blockchain networks, while others are more oriented towards support for private, permissioned networks (consortia networks) where participation and membership is tightly controlled.
Hyperledger is focused on developing blockchain technologies suitable for use in the enterprise. The organization has been established to bring together related and even competing technologies in the expectation that the proximity and common governance will lead to interoperability and gradual consolidation.
Choosing a platform will demand significant research and a clear understanding of your use case and requirements and a good deal of experimentation. At the end of the day, there will be no easy answers.
