I have placed a demonstration for He2 on my homepage. You can download it from:
Basically, you should prepare three files. The first one (let's call it "complete molecule") has all of your atoms and basis sets. The others have all basis sets but only a set of the atoms (let's call them "fragment A" and "fragment B"). These latter files should be prepared in ther following way:
a) prepare your files as usual, using COORD=UNIQUE. Then
b) The basis set should be included explicitly, with all exponents, etc. in $DATA, rather than in $BASIS. Basis sets can be conveniently downloaded from http://www.emsl.pnl.gov/forms/basisform.html
c) Substitute the charge of the atoms which should be absent from the calculation but whose basis functions should be kept.
Run your three files. The real interaction energy between the fragments A and B should be :
FINAL ENERGY "complete molecule" - FINAL ENERGY "fragment A" -FINAL ENERGY "fragment B".
If you compute the energies for separated fragments A and B WITHOUT the extra basis functions on the absent atoms, you get the wrong interaction energy. The difference between the two computed interaction energies is the BSSE.
I hope I have been clear (and that there are no major errors in this post :-)