So I'm just trying to brainstorm different sources of energy/opprotunity costs.

Time

Essentially to use an ability it's going to have a charge up/charge down, where depending on balance you will not be able to move, take action, and/or use skills.   You get "justification" for power by having periods of time where you remove all options to yourself.

cool down

Use  an ability and you won't b able to use it again for anywhere from a couple seconds to a long period of RL time.   justification for power by being weaker in other areas, but with brief periods of changing combat in your favor.

Gear

Can't cut very well with a bow,  you'll do as they did in the old days and toss it down and grab my sword.

Mana/Stamina(sterotyped blue bar)

This is where we start getting into actual energy costs.  You have a nice ability to just take anything down, but afterwards you're going to have to be on the sidelines while you recharge or spend resources to get back in fast.

Focus(sterotyped yellow bar)

You can use lots of skills in a short period of time, do tons of damage or whatever, don't have many cooldowns/charging actions.   but you're gated by a yellow energy bar that acts like a global cooldown/cost and forcing you to make choices instead of just "PRESS EVERYTHING AT ONCE"

Rage(sterotyped red bar)

You're just an angry guy, attacking something just makes you redder, that random mage shooting stuff at ya isn't helping.   After you get yourself all flustered up your ablilities will start to do more things than they did previously, use the right ability and you might calm down for a bit(that mage is still shooting at ya though).

Faith

You serve a greater being that grants you purpose and you perform his great work on earth.   All your abilities start with a 200% casting chance as you start to use your abilities they'll just start to fail as that which you serve becomes fickle.   This is fine though as to better serve you've trained yourself in other great arts.

Combo

It makes perfect sense to yourself that sometimes you just need to wham someone in the face before going for the groin to inflict the most pain possible.   You have great power but there are just those people out there who can distract you from doing your ultimate doom dance of fury.   (some skills can only be used after using others IE: openers and finishers).

Charge up

You have lots of abilities others call weak, but those who would call it strong can't tell stories anymore.  (on the third/whatever use of a skill it has another effect)

Trinkets

You know the ultimate resource mos other fighters don't, they haven't realized that hamer space is awesome and that they should start puting explosives/robots/tools/spellsin their bags.   Sure you may spend lots of time out of combat making stuff, but it's what you would've done anyways.

So I have all the easy things out of the way, what are some other ideas you all have.

LOL, you've killed the conversation.  This is a pretty esoteric subject and by eliminating much if not the low hanging fruit it will be hard to get many people to contribute.  Maybe broadening the discussion a bit to include the presentation/function of those mechanics would help.

About the only item missing that I can see is:

Position

Are you close/far enough to perform that attack?  Are there objects limiting swing arcs (a cover mechanic of sorts)?  These would be matters of position.

Really though, I do think the meat of this subject is in how they are presented.  "Faith" or my pefered term favor for example could be a great downtime/preparation mechanic.  There is something appealing about the idea of making a ritual sacrifice to gain the favor of a deity in a fantasy setting.  BTW, I'm talking active participation by all members not some push buttom buff.  Or as another example a hybrid of "combo" and "charge up", that is were combining 2-3 skills give effects not present in the individual skills (windstrike through a flame wall gives a  DoT where as flame wall only burns while you are in contact with it).

There is also a whole catagory of issues that seem just out of reach to this topic as it is framed.  We could also be discussing the merits and weaknesses of static, dynamic and user selectable costs. 

Exhaustion

Reduced mana regean.   Just going to take a break now.

Burnout

When using a spell your maxium energy is reduced for X time.

Companions

I may not have my golem anymore, but boy are they dead. (AI companion if alive, if dead, explode them).

Health

The enemy shall fear my blood.(health sacrifice)

Enviroment

I feel the storm, rain down thunder.   You thought it was a good idea to hide in tall grass, well it wasn't alive then I guess.(weather, where standing and on what)

Enemy position

You won't be moving while I'm steping on your shadow. So this spell will teleport me halfway to my target, that's all I'll need.

Random chance

I'll call it a goblin punch.  Probably the worst design for a PvP game. (random damage over wide range)

Conditionals

With your own actions I condem you.   You dare use fire against me.  Look at me I'm a rogue I get free dodges. (reflect damage, absorb fire)

Passives

If I don't use this ability I get a bonus, If I use it I get a normal ability.

____________

Done and killed it some more.

To be honest there needs to be a base point for what you consider an actual cost over an inherited mechanic.    

For instance I think you could do a fine job designing a mage with no energy at all and just playing with animation/charge up(locked time before skill)/charge down(locked time after a skill)/cooldowns.   Then toss in skills that have a passive ability when not on cool down, a native gear set of say sword+shield+leather armor.   You now have a character that can be a tank or burst down one enemy.

Where you could have a rogue that has energy that has burnout+exhaustion costs by just passively being near enemies(even without using a skill) and an energy bar closer to mana.  Then has a healthy mix of skills that are very low costs(high cool down) and very high energy costs(very little cool down).    Meaning that the rogue must choose between being an assasin or a nimble+evasive brawler.   This achieved with on the fly decisions rather than forcing players to lock themselves out with skill trees.

This is actually pretty fun just taking 3-4 costs and ignoring everything else.

You seem to be talking about flavor more than mechanics now, and I don't think that's as interesting as where you started.

One of the huuuge opportunity costs that you missed is the obvious one—money. Or rather, consumable items that cost money. These could be ammo for your weapon, reagents for your spells, one-use items that empower one of your abilities, or anything that gives an immediate or prolonged advantage. When you can buy things like these, the question becomes "which of these are worthwhile to keep in stock, and which ones should I pass up? Or should I buy none of them and save my money for other things?"

Defense: Abilities or stances that make you more vulnerable. The penalty should be steep enough that it's clearly not advantageous to use it while trading hits.

Risk: Abilities or stances that are more powerful while you are in more danger. This could take the form of increased damage based on your missing health, a skill that can only be used (or becomes much more powerful) when you are below 25% health, or point-blank AOE spells that are most effective when you are surrounded by enemies.

XP/Levels: Actions that cause to you to undo some of your progress through the levels. Usually a death penalty, but older versions of D&D used this as the crafting system. Making magical items required you to pay XP. This becomes a roundabout way of costing time. Rather than having to do something for half an hour to accomplish a task, you'd incur a debt of half an hour's worth of XP. Note that in a game with an XP penalty for dying, ALL decisions have XP as an opportunity cost because the choice that makes you more likely to die has a potential XP cost associated with it.