First of all, it sounds like a nice idea, but I see a few "flaws" with it:
If we tag it at the end, most OSs will not be able to sort them in explorer or finder or whateverhaveit, and if moved directly to the replay folder, they will still be sorted by the clan of the first lad.
Now, if we had a "tagging system for automatically saved replays" here is a short list of features that could be useful/helpful:
1) A tagging system at the front of the replay name, eg "[Aikido.tbm][Secret]Mysteryvs[Urban]Erth1337-666.rpl" (I will assume that all OSs fully support the integration of figures in the replay names, including punctuation in the form of dots and colons)
2) A tagging system that is customizable with at-least these three features:
a) the date of the replay, including timecode in form of [2013/10/01@14:52:18]
or similar ([2013-10-01@14h52'18''], or any combination of such)
b) the mod as formerly suggested in the form of the whole mod name, [Aikido.tbm]
c) the way someone won; [Pts] or [DQ] or similar (read Points, disqualification etc)
3) A tagging system that allows separation into different folders, mainly to separate the games you've participated in form those games that you did not participate in, and then perhaps even into folders called "Wins" and "Losses" (and "Draws") for a better overview of your replays.
A note on the 3rd way; if a customization-system were implemented as-well, a feature for only saving your wins could also be fun to have for those of us that care little for most autosaves'. (OT: as of right now I just deleted my autosave folder, 1.2 gigs of files that I barely ever notice.. or need.)
Combined: [Aikido.tbm][2013/10/01@14:52:18][DQ][Secret]Mysteryvs[Urban]Erth1337-666.rpl
Now of-course it would be nice if we as said had a customization feature of this so that we could for example disable the timecode if we do not wish to use it all the time, or just that we wish to change the way that the system saves them, in one folder or separating them by wins and losses (for games you've participated in).