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!