I second that, when it's be based on the given total ep-count, it'd also be "001" for ranma/dbz/inu yasha-eps...
When there's no "total eps" given, one *could* assume that it has <10 for movies and OVAs and >=10 for TV-series, but I don't know if that's neccessary
On TV series that run for more than one season, I'd actually prefer <Season#>x<Ep#> notation. See example from Ranma season 1, where I added that in episode names prepended (1x01 <epname>, 1x02 <epname>, and so on). Season two eps would then be 2x01, 2x02, and so on.
do we really need stages in the animeep number?
I mean we could simply add that info in the epname or even use a seperate anime entry for each stage. (and link them using prequel/sequel)