I was asking myself this question just the other day and left it in the too hard basket.
The classic series had it's own production identification. If I recall correctly (per the Target guide that came out early Tom Baker) each story was given a single letter code ("A", "B", "C"...) then the next 26 they went to the same letter twice ("AA", "BB", "CC") then 26 after that they went same letter three times ("AAA", "BBB", "CCC") and finally the next 26 episodes they represented the repition with a number ("4A", "4B", "4C). I think they kept this till the end, but I've also heard that they used alternate production codes too. You could go for story code then episode within story (eg. 4A-2 could be 2nd episode of Robot).
Of course this doesn't tell you which doctor, what year, and other than remembering that Robot was "4A" and guessing Unearthly Child was "A", it doesn't really give you an indication of the story.
And there lies the trick to this question. What do you want the identification to tell you?
If your interested in year and then episode within year then "yyyy-ee" where "yyyy" is the year (to be 2000 compliant) and "ee" is the two digit episode. This works better for the new series because it tends to have mostly single or double episode stories, and each episode has it's unique name anyway.
Likewise the series number + episode number works well, but just leaves you with the arguments about whether to restart the series number and whether to count years where they have a bit of break. Since the classic episodes predate torrenting, it seems that the accepted practice has been to restart the new series from S1 and move on.
Incidently most of the Hartnell episodes had unique names too even though they were all organised into multi-episode stories. They dropped the episodes names, I think towards the end of the season before the one that Troughton arrives in.
The problem for me is that I don't tend to think of the classic series as season + episode. I tend to think of Doctor + Story + Episode, and that's how I identify the classic series. So I use two different schemes, one for classic, one for new.
There was a fan/parody mag, I think called "Ming Mongo" or something that seemed to have a very solid argument for how to identify Dr Who episodes, with reasons for the format that made a lot of sense, but nobody else seemed to use it, so I put it down to even when your right, if everyone else is wrong, your still wrong.