One of the coolest things about molecular modeling is finding the structure of a transition state (TS). It's nearly impossible to do experimentally, and it tells you so much about the reaction mechanism, clues to making catalysts, etc.
You can draw the most crazy initial guess structures for the reactants and products, and upon minimizing in Avogadro you will still have something reasonable. But there are no general force fields that can handle TSs so you have to make the TS guess much like you make a bonsai tree: small adjustment applied with infinite patience, and plenty of water.
The screencast shows how to make a guess for the TS of the Sn2 reaction F- + CH4 => CH3F + H- in Avogadro. The point is not how to choose the TS geometry but how to make it in Avogadro once you have decided what is should look like (how to do that is the subject of another post).
Once the guess is build you need to compute the vibrational frequencies to see if there is an imaginary frequency, and I show how to set up a GAMESS input file for such a calculation at the MP2/6-31++G(d,p) level of theory.
(The screencast was made with Avogadro 0.9.4. 0.9.5 has just been released and looks a little bit different. I haven't even published this post and it is out of date. Welcome to the blogosphere).