The origins of these wars goes all the way back to the beginning of email. The creators of email were clever folks, and gave us numerous headers to denote different roles - From for who the mail is from, Sender for who sent it, To for who it was written to, Cc for who else should be sent a copy, and Reply-To for who the replies should go to if not the author. The problem is then "who do you reply to?" You commonly want to either reply to the author, or to everyone. So mail readers added a reply-all command (I'd say buttons, but mice weren't very common back then, and most users were using character devices) that replied to the To and Cc addresses as well as the From or Reply-To address.
Mail lists - another clever invention - are almost as old as electronic mail. They leverage the electronic nature of email to make it possible to send a message to many people without having to create many physical copies of the mail. However, the standard reply/reply-all commands are insufficient, because there are three reasonable defaults for a reply to mail from a list:
1) The default reply on a discussion list that only members can post to should only go to the list.
2) The default reply on a want ads style list should only go to the author.
3) The default reply on a help list should go to both, as you want to make getting help easy.
With only two reply commands, you clearly can't have all three replies easily available. The normal behavior doesn't have a command to reply to the list. One way to fix this is to use (or abuse, depending) the Reply-To header by setting it the list address on mail to the list. This means a mailer with two reply commands no longer has a way to reply to the author, as that option has been co-opted to reply to the list.
This is the root of the Reply-To war: should a mail list set the Reply-To address on messages or not? Some people believe that should never be the case, and argue that doing this violates the RFCs and breaks software and user expectations. Others believe that this should be the case most of the time, and argue that not doing so is impractical and breaks software and user expectations. Most people don't care - they either view this as just another annoyance of dealing with computers, or have gotten so tired of the discussion that they don't want to hear it again. But a strident few on both sides will bring it up on lists that don't act they way they want, generating replies and flames from the opposition.
Oddly enough, the complaints boil down to the same no matter which side you're on: "The reply commands on my mailer don't behave the way I expect them to for this list." Both sides, in fact, regularly tell the other side to get a better mailer to fix their problems. While this is the right spirit, it applies to both sides once you realize what better really means. The solution has been around since 1998, when RFC 2369 was published, which provided guidelines for adding headers to messages to make list functionality easy to access. Most mail list software now adds a List-Post header that tells you how to post to the list, which contains the address that would be put in the Reply-To header should the list abuse (or use) that. Most mail readers still don't have a way to use the List-Post header, or don't have that enabled by default, and still just offer reply/reply-all commands with the old behaviors, so the old arguments persist.
If you're going to get a better mailer, you should get one that has the functionality you actually need: A reply-list command, that uses the List-Post header; a reply-author command that replies to the From header, ignoring Reply-To in case some mail list set it. And then the old reply-all command, so you actually have all three list replies. Personally, I also have the original reply command, which doesn't ignore Reply-To, for those rare messages that use Reply-To for what it was originally intended for.
So if you're tired of these wars - or tired of inconsistent mail list behavior - check your mailer to see if it supports List-Post, and enable it you need to. If it does, post a comment here telling us what it is. If it doesn't, submit an enhancement request to get that added. And then bug your mail lists to support List-Post if they don't.
Mailers I know support List-Post: Claws-mail, which provides the four commands named above. KMail, which points the reply command at List-Post if it is present, and provides reply-author with the reply behavior.