When building decks, I consider what the "big" cards and mechanics are at the time. Right now, here's a partial list of what I would ensure I had protection against:

• Bouncing (Lord Jeffrey Farrington, Initiate of Huang Hun)
• Destruction (Khopesh, etc.)
• Removal and Forced Commitment (Cavern of Flames, Y'Golonac)
• Characters that enter unexpectedly (Dirk Sharpe, Dreamlands Fanatic, Intervention, etc.)
• Recycling (Unspeakable Resurrection, new Shub's DY ability, Ubuorus or whatever his name is)
• Rushing (Miskatonic anything)

Typical ways to combat that are listed below, but are not limited to these ways:

• Bouncing: bringing out free characters is always a good way to combat bouncing. Dreamlands Fanatics and Rich Widows are great for this. Also, bouncers like Huang and Jeffrey are typically the same faction; use Professor Lake to force multi-faction plays. Professor Lake is also great against a mono-faction deck (such as my wife's Deep Ones deck)
• Destruction: Well, it's hard to combat destruction unless you have control cards from Hastur. Performance Artist, Power Drain, and Writhing Wall are still your best stops for destruction. Having characters with Toughness also helps to an extent (go go Dutch Courage, Twilight Cannibal, etc.)
• Removal and Forced Commitment: since Cavern of Flames is one of the primo removal cards, it is easily combatted with Location/Support control: Torch the Joint, Lodge Housekeeper, Deep One Assault, and Forced Foreclosure are some of my favorites. Forced Commitment via Y'Golonac and that new Agency card in Written and Bound (love that card!) can be combatted through stuff like Behind Bars, Timely Intervention, Kidnapping 101, Ravager of the Deep, etc.
• Unexpected characters: now this is a fun one. Basically rely on destruction or bouncing to keep these out of the loop, or combat them with more unexpected characters, Dirk Sharpe and Master of the Myths being my favorite. Your opponent may think he's got you beat with his shiny new Intervention or Terror of the Tides, but then you play your Haunting... something or other (Yog card, has like a ghostly werewolf as the art) and you're golden. Also, Timely Intervention during a Story Phase will keep some of these triggered characters from popping up.
• Recycling: well, the easiest thing to do is include Snow Graves, but thankfully most recycling decks aren't really tournament viable... yet. Again, Hastur control is usually another safe bet. Power Drain on Peaslee will irritate nerd decks.
• Rushing: well, Nonspeakuh the Latinuh Perimbulus is the premeire rush stopper for now. Panic, Catastrophic Explosion, and In the Wake of the Sleeper are also fun rush stoppers.

All that being said, you want to make sure that your deck has a FOCUS as well. I've seen way too many decks that try to do too many things, and you can't prevent EVERYTHING in one deck. And as dboeren said in another post, play test them against a variety of decks!

Konx wrote some articles a while back regarding cost redux, card economy, and some other stuff, and I'm thankful because he's better about putting those things into words than I am. I freely welcome any questions, comments, critiques, etc. Hope this was at least helpful and didn't come off as overly preachy!

Preachy? Far from it. This was exactly what I needed. Putting card names to current strategies and their counters is great. I still don't know the card pool well enough to be able to envision those things. 

 Would you say that each (most) of the factions have a way to deal with these things? Or at least enough so that MOST combinations of dual faction plus some neutral cards can address most of the likely strategies you'll encounter? 

Each of the factions has their own strengths. Generally, it's necessary to combine 2 factions to get a good spectrum of prevention and win mechanisms. Someone summarized them awhile back, but I'll attempt to do so.

Mythos Factions:

• Cthulhu - Cthulhu is all about destruction. Several events (Feeding Frenzy, Deep One Assault), support cards (Stygian Idol) and characters (Cthulhu, Jade Salesman, Deep One Rising)
• Hastur - Hastur is all about insanity and board control. Cards like Cavern of Flames control who's committed to what stories, while cards like Victoria Glasser can deal with who's gone crazy.
• Yog-Sothoth - One of Yog's strengths is recursion. Early on there was an attempt to make Gugs feasible (and they could be in the future), but really their focus is on deck and discard control. They have some fun cards that force your opponent to choose characters to sacrifice. They have some fun free characters too (Haunting some-or-other-wolf-thing)
• Shub-Niggurath - Shub has some beefy creatures which are fun, but where I think they really shine is in Acceleration and Support Destruction. They have several cards for accelerating resources (Eat Her Young, Eat the Dead), several for character acceleration (One of the Thousand, Priestess of Bubastis) and several for destroying support cards (Burrowing Beneath, Grasping Cthonian). Cthonians are going to be fun if they get pimped just a little bit more, but Shudde M'ell did a lot for making them more viable. The Fungi from Yuggoth are fun as well, since they all work well together... if you can get those Mi-Go rolling.

Human Factions:

• Miskatonic - Miskatonic U is about rushing and card draw. There are too many card drawing cards to name, and they have so many tiny guys as well. They also have some interesting neutralization cards (Flux Stabilizer) and rush-to-win cards (Open for Inspection).
• Agency - The Agency is all about Combat struggles. There are quite a few wounding cards that are awesome (Catastrophic Explosion, Short Fuse, A Small Price to Pay) and some removal cards (Behind Bars, Timely Intervention) that are worth mentioning as well.
• Syndicate - These mobsters' focus is primarly on Skill Reduction (Clover Club Torch Singer, Like a Moth) and Exhaustion (Hard Case, Panic). Kidnapping 101 is also one of my favorite removal cards in the game.
• Silver Twilight - The mysterious order is kind of a mixed bag right now. They have a lot of things that synergize well with other factions, and they are able to fill holes for several decks, but the most fun I've had with them thus far is using them for bouncing. Oh. My. God. I love Lord Jeffrey Farrington and the Initiate of Huang Hun. They are 2 of my favorite cards right now. They also have some interesting surprise characters... most notably Dirk Sharpe and Master of the Myths.

Again, each faction has its strengths, but none of them (except for Cthulhu) does well standing on their own, in my opinion. Some unlikely factions work really well together (Shub/Miskatonic, Hastur/Agency, Syndicate/Cthulhu) if the deck is built properly. Generally speaking though, most Mythos factions work well with each other, and same goes for the Human factions.

The one thing I can't stress enough is to have a theme. My SY/ST Trampoline deck that I posted is all about denial: bouncing and exhaustion. I have just enough stuff to deal with support cards and some rush things to round it out to make it an enjoyable deck to play, and annoying to play against. Hope that this is also helpful.

 I've never been to a Call of Cthulhu tournament before, but I have played some other ccg's on a tournament level before. When it comes to deck building all I can say is that you should focus around the one and only core thing that really matters imo: card advantage. Now this is often missunderstood. This does not = drawing cards. You want to have an advantage on the board. You can achieve this by destruction, take control, drawing, bouncing, exhausting, letting opponent discard cards, etc. Make sure your have a card advantage and you will win more often than you will loose. 

Very helpful and well written article.

@ Mephistopheles: Agreed. Card advantage takes many forms and the same seems to hold true in Cthulhu as it does in Magic. So… a "yeah what he said" +1 to your post.

Thanks for the article, some great thoughts there.

In looking at the list of issues that need to be covered for a deck to be "safe", I think there may be more issues than there are direct fixes.  As such, cards to look for may be those that could potentially solve different problems.  Master of the Myths is a great card (probably too great - Restricted list, here we come) because he can so handily deal with destruction, removal, insanity, etc.  Hard to counter a card that isn't going to be there until the start of the story phase - and that has Willpower and Toughness.  Flux Stabilizer, likewise, helps shut down various flooding and discard pile fishing strategies (and Master of the Myths!)  It's cards like those - that have multiple strategies they can help counter - that will be useful.