Are there any websites that let you model old gear on your character?
Not on your particular character, but Wowhead lets you view any item on the race/gender of your choice.
Blizzard allows us to hide Helms and Cloaks. I've always assumed this is because some of them are butt-ugly, but is there a game-play reason for this, and for why those two things were specifically chosen instead of slots for other things, such as the hideous Champion Herrod's Shoulder?
Helms are able to be hidden because some people are more attached to their character's face than to the helmet that covers it. Cloaks obscure the back of the body, so they're also able to be hidden.
What enchant effect, if any, will be shown on a mogged item? The equipped item's enchant? The mogged item's enchant? In the case of a void storage item, no enchant at all? I've looked all over but haven't seen any information on this, anyone have any idea?
Visual effects (such as Thunderfury's crackle) will persist from the template weapon. Weapon enchants from the base item will persist where possible. Some weapons don't allow particle effects over their default look.
To use an example: Let's say you have two daggers. One of them is the Scaleslicer, which has a sort of fire effect on it, and is enchanted with Landslide. The other is a Core Hound Tooth, unenchanted.
If you transmogrify the Core Hound Tooth to look like your Scaleslicer, the equipped dagger will have the Landslide visual and the fiery particle effect. If you reverse it and make the Scaleslicer look like the Core Hound Tooth, the Landslide visual effect will persist, but the fiery particle effect will not.
EDIT: Apparently this answer is wrong and no effects from the template weapon will appear on the equipped weapon. Sorry for the confusion!
What exactly is the purpose of "You have entered too many instances lately?" 'Cause I gotta say it's really annoying to get to that point when you're trying to farm for gear for Transmogrifying.
It's intended to reduce stress on the instance servers, but, long ago, it also served to prevent botters and hackers from chain-farming chests in instances.
Why (oh, why) isn't Furrier Schnottz the final raid boss of Cataclysm?
Because Schnottz, like nearly the entirety of Uldum, is a lazy reference that actively detracts from the quality of the game it's now unfortunately a permanent part of.
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