Well, just off the top of my head, Naxxramas. Not a big deal, but it is still a full retcon. What was originally the heroes of Azeroth joining together and burning the citadel to the ground becomes Darion leading a strike force inside to reclaim the Ashbringer, with Naxxramas warping out back to Northrend shortly afterwards. It could've been worse, but it really felt like more of an actual, depressing bummer than "RAGE" that the epic efforts put forth were 'toned down' and then played again shortly before Wrath's release. And to be honest, it was really bummer to see an instance that was once a veritable river of raiding tears reduced to sub-Kara level of difficulty and simplicity.

Garona's kid is another issue: Argument about bloodline aside, and timelines for her to be birthed by human and orc blood--this is assuming that Llane really truly was the father, and I heavily doubt this. Llane was a good friend, but a better man than to be sleeping around with a sleazy half-orc assassin/spy.

Mal'Ganis surviving is something else. I can understand Balnazzar, seeing how Varimathras was duping Sylvanas all along, but Arthas truly, purely desired nothing more than to end Mal'ganis. As consumed with vengeance as Arthas was? Frostmourne in hand? Nathrezim must carry ankhs around or something.

And it isn't so much the retconning as the stretching of things, beyond the growing pains of an expanding universe. Wrynn's whole story, for example, up to this point doesn't sit well with me, namely the slavery issue. I very much doubt that, even in a pure warrior society, the orcs would condone complete slavery, seeing as how they were once slaves to demons. And a shaman taking part in it? Not so much the virtuous man card in check here as what is expected of the shaman and his/her bond with the elements.

Eh, although I wouldn't put it past Blizzard to just ignore that line and have us go around killing more Old Gods in every new Azeroth-based expansion, I imagine that at this point they do have a coherent idea of what the Old Gods are and how their nature will be revealed throughout the content. And we could imagine any number of stories where it turns out that killing the Old Gods does have catastrophic effects - maybe they're just relatively benign parasites that are holding back some more-problematic Really Old God, or maybe Azeroth will start dying and we'll have to find a way to fix whatever the Old Gods' presence had kept stable, or something or other.

Just my take on it, but I have a feeling that since the Old Gods were responsible for the curse of flesh, it might be that if they all die, the curse itself is "lifted", but in a way that causes all life affected by it to basically just flop over dead or turn to lifeless stone (or something more gruesome..).
Again, hopefully it becomes a central theme to a future expansion!

We have to wait for more lore to come forward, but I'm starting to suspect that there is a stronger connection between the titans and the Old Gods than possibly has been admitted. Perhaps the issue isn't that the Old Gods cannot be killed, but that the Titans cannot, for whatever reason, kill them. And the killing of them may bring the Titans attention on Azeroth, but not necessary for the apocalyptic reasons we envision.