We are developing a new technology; A way of doing things differently than they have ever been done before, with the Blockchain and Bitcoin.
It is obvious that as we progress further down the path that Bitcoin and it's blockchain concept allow, complexity will give rise to a sort of entropy of method because of the availability of many more disruptive technologies; Technologies such as hashes, cyphers, Homomorphic encryption, Magnet links, etc.
This allows us to create Blocks within Blocks linking to Blocks of information on not just one but multiple Blockchains linked together or transactions linked together. Information simply being itself, linking and forming as it is most apparent.
What am I talking about? Megablocks: Blockchains with separate information perogatives linked to other dynamically generated Blockchains, Hyperchains: Transactions linked across Blockchains, and Proxy Blockchains: Blockchains secured by other Blockchains, different than Mergemining, Ephemeral Blockchains: Blockchains created inside Blockchains.
With this, new forms of Blockchains will arise linking their state, referencing each other in a secure decentralized manner, forming dynamic minichains, hashing of blockchains into blockchains for security, Magnet linking blockchain states, a multistructure web of Blockchains.
https://bitpay.com/chaindb.pdfChainDB does a lot of what you're talking about - other blockchains referenced inside of Bitcoin's blockchain.