(With no context at all it's difficult to provide a concrete answer - you may want to provide more information in your question)
Most decent mail user agents (MUA) use the In-Reply-To: header to indicate message threading, without resorting to unsafe operations such as parsing the Subject: header. Most such clients also have a proper threading mode where unusual stuff such as Re[2]: is at best unnecessary. The de facto standard of using Re: is a good compromise between terseness and content, but with proper threading support it eventually comes down to aesthetics.
Just use Re: in messages you create yourself - anything else is bound to lead to confusion. Make sure you properly generate the In-Reply-To: header for any reply messages.
Please do not remove content from the Subject: header. You may refrain from adding to it when e.g. a proper Re: substring already exists, but if you are actually removing strings you are bound to get it wrong, leading to confusing situations.
This is not a strictly technical issue - different people have different preferences. In a specific community, e.g. a mailing list, social automation (sic) will take care of any repeat offender that uses strange or confusing conventions.
Trying to deal with this automatically is bound to cause more problems than it would solve. Such issues are also not the responsibility of the carrier - i.e. the mailing system. Keep your system simple and focus on real technical problems.
EDIT:
A common case of a broken client (or user - I have always been unclear on this) is the Re: avalanche case:
Subject: Re: Re: Re: Re: Re: Re: Re: Re: Re: Re: Re: Re: What about that thing we were talking about?
Tempting isn't it? A simple filter rule in the MTA, or a few lines of code in a replying MUA and the avalanche is replaced by a nice, single Re: automatically!
In my opinion, this is one case where the temptation should be resisted to:
There is no guarantee that an MTA is the only path a specific message uses. For example, when some users reply to mailing list messages, they reply both to the mailing list and directly to the poster. Naturally, the poster will receive both messages, most probably by completely different paths.
Do you know how confusing it can be to receive the same message with two different subject lines? Even a basic sort-by-subject would fail. In my opinion, even spam detection systems that add [SPAM], **SPAM**, $P@M or whatever to the subject are pushing it.
Can you imagine a library selectively changing the titles of their book copies according to some sort of local policy?
Even if your MUA "fixes" the issue, everyone else will still be using the old subject, except for when replying to you. Moreover, you have just single-sidedly created what appears to be a new thread. Proper mail clients will still display the thread correctly, but the visual effect is confusing. After all, you did remove a highly distinctive feature of this thread from your reply post, didn't you?
I actually remember a couple of fun threads where the Re: avalanche in their subject was part of a tongue-in-cheek discussion. Why would you want to miss on that?
Sure, people use broken clients. Or they are broken themselves. If anyone gets really out of line it can be handled individually. Just don't compound the problem and leave our Subject: headers alone. Please? Pretty please?
