mhh... a lot of things increase your dps and you already listed most things that do but I'll list them in a bit more detail for you:
Upgrades: You should already have your gold upgrades maxed or close to it after that spent most of your gold on Auto Upgrades and invest your AP only in Auto Speed cause the gold cost gets way to high.
Orbs: Auto Orb and Crit Orb both increase your DPS but the auto orb is better but you most likely already know that you shouldnt only get this 2 Orbs. I don't know what Orbs other people got first but I would probably buy them in this order: Auto, XP, Crit, Gold and after that its up to you some people go for Wood/Mining others for Pets.
Cards: Farm 100 cards per zone on your first round threw all the worlds and then always go for the next milestone.
Inferno bonus: you get the dmg boost shown on your character page + a 2.5% dmg boost for every level above 200.
Guild Upgrades: to be honest you shouldnt buy the dmg one. Most efficent way to spent guild XP would be to buy the XP upgrade and a few levels of the gold uprgade, some people buy the pet upgrade but in my opinion its not worth it at the moment.
Challenges: You get Challenge Points for every monster you kill for the first time and a Challenge Bonus for every Challenge you complete for the first time. Challenge Points give you a % bonus for hitting milestones (I think its 3% per milestone but I'm not sure about the lower ones). In the Series Challenge you get 1CP for every monster you kill for the first timem 1% dmg boost for every 10th monster and 5% for every 50th monster ( You get both bonuses for every 50th monster meaning you get a total of 6% for them).
Pets: They also increase your dps but after level 200 they become insignificant unless you spent a lot of real money on the game to level them. In my opinion max arena slowly (I wouldnt spent more than 50AP per level) and don't worry about them until they get another boost.
I hope that explained a few things for you.
Upgrades: You should already have your gold upgrades maxed or close to it after that spent most of your gold on Auto Upgrades and invest your AP only in Auto Speed cause the gold cost gets way to high.
Orbs: Auto Orb and Crit Orb both increase your DPS but the auto orb is better but you most likely already know that you shouldnt only get this 2 Orbs. I don't know what Orbs other people got first but I would probably buy them in this order: Auto, XP, Crit, Gold and after that its up to you some people go for Wood/Mining others for Pets.
Cards: Farm 100 cards per zone on your first round threw all the worlds and then always go for the next milestone.
Inferno bonus: you get the dmg boost shown on your character page + a 2.5% dmg boost for every level above 200.
Guild Upgrades: to be honest you shouldnt buy the dmg one. Most efficent way to spent guild XP would be to buy the XP upgrade and a few levels of the gold uprgade, some people buy the pet upgrade but in my opinion its not worth it at the moment.
Challenges: You get Challenge Points for every monster you kill for the first time and a Challenge Bonus for every Challenge you complete for the first time. Challenge Points give you a % bonus for hitting milestones (I think its 3% per milestone but I'm not sure about the lower ones). In the Series Challenge you get 1CP for every monster you kill for the first timem 1% dmg boost for every 10th monster and 5% for every 50th monster ( You get both bonuses for every 50th monster meaning you get a total of 6% for them).
Pets: They also increase your dps but after level 200 they become insignificant unless you spent a lot of real money on the game to level them. In my opinion max arena slowly (I wouldnt spent more than 50AP per level) and don't worry about them until they get another boost.
I hope that explained a few things for you.