Step 1. The job you want it to do. You can use them to capture, kill sectors, OOS/ Sector Patrol, Personal ship, Other, ETC ETC.
Step 2. Choose your M6.
There are 5 M6s in the game,
Argon Centaur- a good all rounder has decent guns, decent speed, and good shielding and is cheap. Only 7 million credits.
Boron Hydra- A fast and decently shielded, but poorly armed and extremely expensive 9.9 Million!!
Paranid Nemesis- A fast and deadly. Has good shields, the ability to mount Gamma PSGs, and fast. But has a really small cargo bay. Only 8.4 Million Credits
Split Dragon- Fast, Deadly, and Powerful.This ship is fun to fly and handles like an M4! It can mount heavy guns and is fast. It has low shields though. It is the cheapest M6 in the game. Only 6.1 Million Credits!!!!!!!
Teladi Osprey- A tank, the most heavily shielded M6 has the most turrets/ weapon mounts of all the M6s. Can kill if you can reach the target! It can mount up to Beta PSGs. The slowest M6 of them all. Only 8.9 Million Credits.
Step 3. Getting the job done. Now you know what you want your M6 to do you need to know which ones fit what you want to do.
For ship capping the Centaur is good for its ability to mount Beta PACs and Mass Drivers and it has decent shields (250Mw) and an ok speed (207m/s) Good for capping M4s, M3s, And TSs. The Nemesis is good also Because it has the same shielding as a Centaur and can hold Beta PACs and Alpha PSGs which are good for capturing and is fast (250m/s).
For Sector Patrol/OOS the Dragon is good for its speed and its guns. It can catch most M5s and M4s. The Centaur is good for OOS because it has good speed and good guns. Ive found that Sector Patrols work good in pairs. I use Dragon/Centaur patrols for the most effectiveness. The Hydra is an option too for its ability to mount Ion Disruptors.
For OOS there are three things that most players want
1.shields needed to protect the ship the bigger the shields the better.
2.weapons- needed to pack a punch for killing larger ships
3. speed- need this for catching up with M4s and M5s.
Kill Sectors- The Dragon and The Nemesis are the two for this job. The Dragon for the Guns and speed. If you are using the dragon to clear sectors with M1/M2s Watch the shields on the dragon they go down quick. The Nemesis is good for Killing sectors because of th Gamma PSGs and good shields.
Personal Ships- This is dependent on what you want to do with it the best choice is to look them up and compare them and see which on you want to use. Look them up here at the argonopedia http://argonopedia.ppcis.org/.
Hope this helps and is useful in deciding what to do with your M6.
Suggestions or corrections appreciated

Thanks to these people for suggestions/corrections
Fed-Up for some info on the dragon and the osprey.
JCTiger- for info on OOS fighting