I think if the only goal is to reduce misinterpretations or incompatabilities, you should use version numbers without digits. Just counting from 1 (or 0) will do. Some people use YYYYMMDDhhmm. DNS uses YYYYMMDDXX, with XX starting at 01 and incrementing to 99 for updates happening the same day.
in reply to module version numbers
The reason is that Perl considers '1.2' a newer version than '1.19' - '1.2' being a shorthand for '1.200', and '1.19' a shorthand for '1.190'. And that's fine when all you have to care about is Perl and its common infrastructure. But if you interact with tools or people that aren't focussed on Perl, you may encounter tools or people who consider '1.2' an older version than '1.19'.
I'm not claiming one system is better than the other. (Although considering '1.2' newer than '1.19', but '1.19.0' to be newer than '1.2.0' is something I find confusing). Just that eliminating dots has its benefits.
Of course, that way you lose the convention that the more dots after the incremented number changes, the bigger the change is. But I've seen small projects using version numbers like 220.127.116.11 which makes me wonder what kind of change bumps the version to 18.104.22.168 and what kind of change bumps it to 22.214.171.124. Or 126.96.36.199.