Pete,
Like Jon said, a good idea to leave 2 or three nodes on the branches (don't prune all the way back to the trunk). If it's a tree that you want a breba crop from, then leave more branches unpruned. As for the secondary/tertiary branches, I'd suggest be guided by the shape and size you're trying to achieve. (And size of the top depends on what you can do for the roots... as Al Tapla and others have pointed out, this potted fruit tree business is a lot like bonsai).
I couldn't tell if you're also asking a related question: what time of year makes sense to prune a tree if you're interested primarily in the health of the mother tree for the coming season (versus interested in the ability to propagate the cuttings). I like Ingevald's advice from this perspective too... he said early spring just before waking up seems optimal. I like that because it also is the time that leaves the least risk to the part of the branch remaining on the tree. I still do fall pruning too because of practical reasons (i.e. the practical aspects of protecting a tree through the cold cold winters here... it's easier to "store and protect" a pruned tree than one that has a big top. Also the reason that it's convenient for trading cuttings with people, to have fall cuttings taken just after dormancy, though for me that is a newer reason than the other one :-). So although I still do fall pruning, that puts the remaining part of the branch still on the tree at an increased risk of winter die-back... as you've probably seen that sometimes a pruned branch will die back to where it branched off.
So what's the best time to prune? It depends... if my only concern were health of the pruned mother tree, I'd choose early spring. But other practical considerations make fall (just after dormancy) also attractive, and in this cold clime where I live, I do that a lot, to prepare for wintering over. The cuttings taken at either time seem able to be rooted.
[[Edit at 3:20PM 11/1/2012 -- Just in case anyone else from a cold climate references this thread some time: let me add that if health of the mother tree branches is a consideration, I'd also consider pruning earlier in the fall, to give the cut end a chance to harden off before the harsh winter hits. The main reason I don't do that so much is because at that point in the year I've still got figs on the tree that are trying to ripen, and pruning too early would interfere with that. ]]
Mike central NY state, zone 5