This is a very quick solution to setting your mesh to T pose in blender. I assume you have imported a rigged human model into Blender (for example using the MHX format).
(This is the approach with manual posing, see next reply for the automated method)
1) In pose mode, pose the armature so that the human is in T stance
2) Exit pose mode, and go to Object mode.
3) Select the human MESH (not the armature)
4) Remove any shapekeys. Blender does not allow modifying your mesh with them, so they will have to go. In the shapekeys panel press the "-" icon until the list is empty.
5) in the Modifiers panel (which is usually to the right of your screen), click Apply on the ARMATURE modifier.
6) Add a new Armature modifier to the stack (click Add modifier) and attach it to the correct armature again (select your armature from the Object dropdown)
7) Select the armature again, go to Pose mode again.
8) Press SPACE and search for "apply pose as rest pose", hit enter
Now your armature should be in T pose, and your basemesh should fit the T stance. We have not applied any special geometry deformations, so posing the armature with arms down should give realistic joint geometry around the shoulders.
If you prefer watching a video tutorial of this: https://www.youtube.com/watch?v=M9y6kzk69f4
To Thomas: maybe one of the blender scripts (the mocap script?) could offer a one-click button to do this?