I went through all the elements and found the cards that could give us the most trouble.
We can hopefully use this to narrow down the cards we need to counter these, so we could possible use the same cards in different situations. Thus not having to waste as much space in our vault.
If I missed any let me know and I'll add them.
(some of it may seem redundant or obvious, but I figured this could help speed up the process a little)
4vd 4vg 4vl 4vn 52r 55r 55v 592 593 595 5c4 5f8 5i9 5ib 5lg 5li 5oh 5ol 5oo 5rk 5ro 5uu 61r 61t 61u 622
Entropy
Maxwell's D - Fire creatures can easily be taken out by this card.
Recommended counter: Fire Bolt, CC
Dissipation Shield - Shouldn't cause too much of a problem for Fire. Rush would be to fast (usually) and Fire Bolt decks wouldn't be affected at all. The only real problem could be if it came out late and held off the damage just long enough.
Recommended counter: Deflagration, Fire Bolt
Discord - Immolation shouldn't have any trouble against this card. Fractal Dragon and Fire Bolt decks could be slowed by this card.
Recommended counter: Deflagration
Antimatter - Immolation counters this card very well. Just be sure you don't run out of them. Steam Machine works well against Purple Nymphs if anyone plays them.
Recommended counter: Immolation, (to a lesser extent) Steam Machine
Death
Bonewall - This card is always a pain when you don't have a lot of creatures on the board. It's expensive to put out, at a cost of 7, but in a nearly mono-Death deck; you might have to get through several of them before you can start doing some serious damage. It can also prevent Rain of Fire and Immolation from being played. Fire Bolt decks could care less about this Shield.
Recommended counter: Fractal, Momentum, Fire Bolt
Gravity
Otyugh - The self-proclaimed muncher of hopes and dreams. I doubt this little guy will see much play outside of the Gravity camp. With Quintessence though, he could quickly become a problem with Fire's low health creatures. Fire Bolt decks will starve him.
Recommended counter: Fire Bolt, Fire Shield
Black Hole - Also an easy card to counter. If we suspect an opponent might play this card we can just not play Immolation. Granted it still wouldn't hurt that much, but it could give the opponent just enough life to survive for the win.
Recommended counter: [Don't play Immolation.]
Earth
Enchant Artifact - Not much can be done to prevent this card from being played. That being said, it could only really become a problem when combined with another permanent from this list.
Recommended counter: Destroy the permanent before they protect it.
Earthquake - Most other elements could find a problem with this card, but not fire. Because you can't Earthquake an Immolation. Fire Bolts would probably have some issues with no Pillars/Pendulums.
Recommended counter: Immolation, Enchant Artifact.
Basilisk Blood - Immolation is a perfect counter to this card. Fractal can spam more creatures that can be Basilisk Blooded. Fire Bolt decks aren't afraid of this card at all. If you're using an Immolation deck and you suspect this card might be played, save them it you can.
Recommended counter: Immolation
Life
Emerald Shield - Can completely shut down a Fire Bolt deck. However, a Fire Bolt deck can play an Emerald/Reflective Shield and 'bounce' the spell off himself to hit the opponent.
Recommended counter: Emerald Shield, Reflective Shield
Fire
Rain of Fire - With all Fire creatures being low in health, this card can really hurt. The good thing is WE ARE FIRE. Other elements might use this card, since it's the best mass-creature-control (CC) card in the game. Phoenix's aren't really worried about this card. Fire Bolt decks aren't affected.
Recommended counter: Phoenix, Fire Bolt
Water
Ice Shield - Being frozen is a pain and can cost games. Immolation can counter this a little.. same with Fractal decks. Deflagration makes it go away. Fire Bolt isn't worried about this card. Momentum isn't really necessary in this situation.
Recommended counter: Deflagration, Fire Bolt
Arctic Squid - Can freeze a lot of creatures if left unchecked. Just one of these can keep 4 creatures from doing any damage. Good thing is they're weak and any CC can take them out. Fire Bolts aren't affected.
Recommended counter: Any CC, Fire Shield
Light
Reflective Shield - Can completely shut down a Fire Bolt deck. However, a Fire Bolt deck can play an Emerald/Reflective Shield and 'bounce' the spell off himself to hit the opponent.
Recommended counter: Emerald Shield, Reflective Shield
Miracle - Fire can usually out-rush a deck using Miracles. Other than that, there really isn't a counter to it. Destroying Pillars.. if we wanted to go that route. Fire Bolts destroy Miracles.
Recommended counter: Fire Bolts, Fire rush, Destroying Pillars
Air
Thunderstorm - This may not present too much of a problem, but a whole army of Phoenix could be taken out. Other than that, shouldn't have to worry about this too much. Fire Bolt decks don't have to worry about this.
Recommended counter: Fire Bolts, [Phoenix still isn't too bad]
Owl's Eye - This card can kill any Fire creature in one shot [except Red Nymph]. Fire Bolts don't care.
Recommended counter: Deflagrations, Fire Bolts
Wings - This counters Lava Golems and Fahrenheigts. Everything won't have a problem with it.
Recommended counter: Play anything that's flying or a Fire Bolt deck.
Time
Reverse Time/Eternity - These cards could really hurt an Immolation deck.
Recommended counter: Deflagrations, Fire Bolt
Darkness
Liquid Shadow - This can kill a Phoenix or a Lava Golem in one turn, but it isn't too much to worry about.
Recommended counter: Crimson Dragon, Fire Bolt
Aether
Parallel Universe - Copying a big Fire creature could be a pain. Shouldn't have to worry too much about this card. One or two are really game winners.
Recommended counter: Fire Bolt
Dimension Shield - Such an evil card, but Fire has ways around it. Deflagration can destroy it. Fire Bolts don't care about it.
Recommended counter: Deflagration, Fire Bolt
Lobotomizer - Really only painful when used with other cards.
Recommended counter: Deflagration
Fractal - I'm almost positive that most vaults will carry a maximum amount of these cards. Firestorm could kill the creatures just as fast as they were put out.
Recommended counter: Firestorm
As seen.. most things can be countered with Fire cards (that's why it's the best element)
Any other thoughts?