Every time I venture out on a mission I do a run-through of weapons and armour for all my companions. Simply make sure everyone is using/wearing the best that you have. Some will be too high a level for you to equip, so it's okay to hang on to them (because there is no storage chest in this game - grrrr...), and it's acceptable to hang on to an extra staff or two to make sure your mages have the full range of elemental weapons between them, but sell all the rest. If it's not the best, it's vendor trash.
I try to follow a similar rule of thumb for accessories and upgrades, though there is more wiggle room here for hanging on to things you honestly think will be more relevant and useful later. But try to be strict with yourself and don't let them build up too much.
I'm fairly sure the sort of items Kotaku is talking about will come under 'valuables'. And while certain things like jewellery and totems can be sold, things like spider ichor and spider glands can be used later for potions and requisition items, and creature research items should be given to a research specialist.