> I have some domains/sites not so popular (not in the first 100k Alexa domains). I will only hear about "Handshake" in 5 years time when Handshake completely replaced what we are using today, by which time, someone else might have "registered my domain names". What do I do? Obviously I can prove I own my .com/.net.

This is one part that Handshake does not explain very well. The existing domains and tlds that icann owns will continue to work moving forward. The top 100k Alexa domains bit works like this:

For the top 100k alexa domains, the owner receives the root of the domain as a domain in Handshake (ex: the owner of `example.com` receives the domain `example` in Handshake). All `*.com`, etc domains continue to operate as they have in the past.