In most isometric games that have character animation, the sprites are rendered from a 3D model with animation, hence there is little redundant work should anything change happen during production such as change of an animation sequence. So the equipments are naturally fit on to a 3D model and can be swapped in an out for other equipments, and then rendered again for various animation, usually without the body beneath.

Here's roughly how it works

1. you have base animation of a character run, idle, attack (3 naked body animations x 8 directions)
2. then you have equipment 1 rigged onto the model and render 3 more animations for run, idle, attack (3 equipment 1 animations x 8 directions)
3. do the same for the next piece of equipment etc.

A few things to note, with 8 direction sprites 3 directions are mirrored from the other ones so you don't need to render all 8 directions. a lot of 2D games are also rendered that look 2D, but there are games I believe that would draw them too with few directions such as some face book flash games, it works the same way, except it is very tedious work to draw them.

If you need Isometric map items such as rock trees and other props for your game you can check our isometric game assets from Super Game Asset.

http://supergameasset.com/nature

Let me know what kind do you need, we have a lot of game resource in our database that is not up yet.

Dofus, and presumably Wakfu, are actually 2D vector art, not 3D. Certainly you could accomplish the same thing with 3D. But the way vector art equipment is made for an isometric game is that one versions of the equipment is drawn (over an example character) for each of the two diagonal sprite directions (away/up and toward/down). Then either a sprite sheet workflow can be used or a bone animation workflow can be used. Dofus, as a Flash game, used bone animation afaik. In either case the image of the gear is positioned correctly on top of the example character for each animation frame of key frame. If necessary the lines of the vector image can easily be tweaked a little to fit a particular frame or movement. But it is not re-drawn. Then, the positioning that has been established for the example character is compared to other characters (rather, an example of each race, gender, and class), to see if it still works. If a change is necessary, a second copy of the gear animation is made for that race or gender or class or whatever. Once the positioning and animation for a type of clothing, e.g. a cloak, has been established for all character types, it can usually be copied for all new cloaks. Similarly, once a tassel has been animated it can be used in a variety of places, like on top of a helmet or on shoulders of armor or as part of an animated background involving tasseled furniture or tents.

I should probably make a tutorial article about this... except I'm not actually all that good at animation. Especially isometric. Best isometric sprite I've done so far is this, with its awkward movement and perspective.

But basically, first you need to decide the size and angle of the tiles the units stand on. Then you need a reference image of a person or animal facing each of the two directions. Then you need to know the art style: whether you are using lineart or not, the proportions, and the color palette. Then you use Inkscape or Illustrator or Flash to do a rough drawing of the unit, with each moving part as a separate group of shapes. For example in Dofus a cloak is made is a few segments so it can undulate. Hairstyles are the same way, assuming they are for avatars or multiple units instead of only one kind of unit. You can draw a box around the unit to help keep different frames synchronized if you are exporting them to png, gif, or some sprite sheet format. Alternatively you save a whole animation as an flv or something like that. And you make a list of the different animations you need for the unit - bouncing in place, walking or marching, some standard actions like swinging a weapon or tool. Getting an avatar base to do all this is the hard part; clothing that avatar afterwards is comparatively easy.