http://www.texfaq.org/FAQ-TeXfuture> Knuth has declared that he will do no further development of TeX; he will continue to fix any bugs that are reported to him (though bugs are rare). This decision was made soon after TeX version 3.0 was released; at each bug-fix release the version number acquires one more digit, so that it tends to the limit π (at the time of writing, Knuth’s latest release is version 3.1415926).
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Personally I prefer separated major.minor.patch format, and I like when a project knows how many of each kind of release they tend to do for a given generation so they use an appropriate number of leading zeroes. As in I'd much rather see 2.099 followed by 2.100 rather than 2.99 followed by 2.100.
That said as long as it provides a logical distinction that is obvious when looking at past release numbers I don't care all that much what a given project chooses.
