How should I prepare e-prints (pre-prints and post-prints) of already published papers?
One thing I suggest is do not put up the paper in submitted-manuscript form. You are free to change from double-spaced (if that is the case) back to single spaced (or as appropriate); you can put figures and tables where they belong; you can use a nice typeface; you can even change the referencing style to a one you like better. 

Use the version that incorporates changes suggested by the referee if at all possible. My guess is you didn't sign away rights until after you made said changes and sent it back to the journal -- or this may have happened, and it may be that the original submission came with agreeing to terms that include all rights in various versions of the paper in the case of acceptance - I hate these types of journals. In any case, knowing your field would help regarding advice here.

This website can help you find out if you are allowed the post-referee-comments version: http://rchive.it/ (it uses Sherpa/Romeo data), but the ultimate answer will come from the journal website.

This will make your paper more pleasant to read, and help dispel the myth that preprints are ugly.