I chose my skills based on bonuses that the companions have. It works out pretty well. I plan to just mail large quantities of mats to the toons that need them.
On Cecylien I have: Cybertech, Scavenging, and Underworld Trading.
The scavenging and Underworld Trading bring me a lot because of Bowdaar's and Corso's bonuses. I work on Cybertech once in awhile, but it won't be viable until after 1.2 when the mounts stop binding to you after you make them.
On Amixin I have: Slicing, Treasure hunting, and Archeology.
The Slicing is to make money for my whole account. I've found that whenever I'm short on money on either toon, I can send all three companions off on slicing missions, come back in half an hour, and then have a bunch of money. I sell pretty much everything I get from Treasure hunting and Archeology.
I'm going to create a Trooper to do these ones: Biochem, Diplomacy, Bioanalysis.