Some truly ancient flamewars, all of which have been around for a couple of decades at least, some as long as half a century:
Unix vs. ITS. Yes, ITS is in the dustbin of history because it was written for a platform which nobody has seriously used in something like 20 years. ITS grognards, however, will still go into a foaming rage at any hint that Unix might be a better choice. And Unix grognards will go into screaming hissy fits at any hint that perhaps the "innovations" they attribute to their favorite hack might have existed long before it.
EMACS vs. VI. Wanna disrupt any technical forum you like? Wait for someone to mention EMACS or VI and then casually say one of the following (depending on which is mentioned first): "I really don't like EMACS. Alt-Meta-Shift-Bucky-Bucky-One is just not a user interface." "VI really lacks anything to recommend it as a developer's editor. Between the anemic scripting capabilities and the hideous, irritating modal setup, you can't get anything done without your editor biting your fingers off." Then just sit back and watch the flames leap up until either the forum is rendered absolutely useless or the mods step in and start kicking butt. While expressing their own preference. (Bonus points if you can get the mods fighting each other!)
Lots of other editors, from very lightweight to overcomplicated, somewhat eased, or at least blurred, this.
Lisp vs. a lot of C-derived languages. (Smalltalk as well—and they have historic ties to the LISP community. This is not without justification, on both sides—Lisp is conceptually different—and cleaner, more powerful, etc.—than most C-derived languages, however, as it is older than many of them, it is criticized for its (parenthesis-heavy) syntax, and as its spec hasn't been updated since 1994, many claim it is obsolete (which it isn't—it's aged pretty well), as well as insecurity from smug lispers).
"Which Linux distro is better?" or "Linux vs. Windows" or "Microsoft is evil/no it isn't/yes it is" can generate epic flame wars sometimes.
There's also Mac vs. PC, or Elitist fags vs. Moronic man-children in the fanatics' eyes. Linux fans tend to be too dismissive of Mac and "macbook users" to argue with Mac fans, though OS Mach still being *NIX sometimes makes an alliance vs. the Windows crowd. These debates can get so intense that we had to consign Microsoft as a company to the Permanent Red Link Club on This Very Wiki when they started up here.
Direct Rendering Manager? (i.e. this brings us to the part about Linux vs. Windows).
But since we have a choice, which desktop environment? Gnome, KDE, LXDE, Xfce, Compiz? That wasn't too hot, but things got much more lively when freshly baked Unity dropped in the middle of Ubuntu. Unity is very much Love It or Hate It — is it the desktop environment revolution or a pile of widgets glued with Mac love, not fit even for LiveCD?
Mac vs. PC. Est. 1981.
Macs first appeared in 1984.
Unless you count the Apple Lisa, which predated the Mac by a few years. Or the Apple I, II, III, etc., which were driven by CLIs instead of the now-standard GUIs.
CLI vs. GUI. Command line users trumpet the superior freedom and customization options of a CLI, while graphical users like to have things like a window system and a mouse.
iOS vs Android. Used to be vs Black Berry to a lesser extent, but the other two are the primary combatants today. This one's only been around a few years, because smartphones have only been around a few years.
Linux vs. Minix.
This was the subject of an infamous debate between Andrew Tanenbaum and Linus Torvalds on the Usenet discussion group "comp.os.minix" way back in 1992. You can read it here!