When you complete missions many times you are offered a choice between the current worlds commendation and either some companion gear or personal gear. With crafting and the galactic market, how much are those commendations worth compared to that gear?
The world commendation gear usually lines up with the end of that planet's levels. So if you get much beyond the high end of the planet's difficulty level, then trading up makes sense.
For example, Ord Mantell (1-10) commendations aren't too useful if you're level 25, since few of the Ord Mantell commendation items will be an upgrade for you at that point.
All planetary commendations have been collapsed into Common Data Crystals, and the prices of mods have been greatly reduced. This means that it is far and away much better to take comms rather than gear. You should always have enough comms to buy new mods, and modded-out gear at level will always beat the standard green items given as quest rewards.