Magical Artisan from Forgotten Realms is very nice in E6, apply it to the Eberron Artisan feats and you can drastically reduce the cost of item creation, enough to make creating the low level Constructs worth it.
Knowledge Devotion is good for increasing the to hit and damage if you're going to be a melee or archer artificer.
Wedded to History [Golden Ager] and Voice of the Master from Dragon 354 are fun. The first makes UMD always a class skill and you only suffer a mishap on a failure of 15 or more. Second allows you to make a UMD check to change the orders of Constructs or Undead as long as their original master's are not present. Useful when exploring ancient ruins or burial grounds and taking what should be near impossible fight monsters and making them yours. Iron Golem or Bloodhulks for example. DC is really tough though so you'd want to maximize UMD as much as possible.
Items I love to make as an artificer are:
Collar of Perpetual Attendance - from one of the Dragon, gives a continuous unseen servant, 2000gp
Collar of Unseen Crafter - make it an at will item and out build anything except at will fabricate. Each casting at minimum caster level lasts 3 days and performs mundane crafting per your check, use multiple castings to Aid Another and stack on the +2's so you can speed up the crafting time. 10800gp Earns its cost back in days if you use it to make poisons, boats, weapons, armor etc.
Bolter - at will item of launch bolt, launch item, based on a repeating hand or light crossbow its my version of a D&D shotgun/grenade launcher. Magically fires crossbow bolts and alchemy items 100ft. 2700gp I like to combine with an internal Quiver of Ehlonna in normal games to make it have voice activated ammunition types. Although it would have to be used with shrink item instead in E6 since Leomunds chest isn't available as a prerequisite spell.
Humunuculos - standard MM version, hide it in your bag and simply milk it for the sleep poison. Trade its feat for Ability Focus Venom.
In one of the Dragon's there is also an enhancement that can be added to Constructs that are normally unintelligent to grant them an intelligence score based on your caster level. I think its something like 1 point per 2 caster levels. So they'd have animal intelligence in e6, not great until you remember that its lack of int that prevents constructs from gaining Feats and Skill points based on their HD.