My friend and I finally got our first Call of Cthulhu Core Set, and we chose our starting factions, taking the appropriate cards from the pool. She is playing Agency and Syndicate; and I am playing Miskatonic U and Shub-Niggurath. Obviously decks are going to vary by playstyle, and even from player to player, but I was just wondering if there were some iconic cards we should look out for in these factions, and what sets or Asylum Packs they come from (if possible, also list the quantity included). We're planning to participate in the Cube Draft at Arkham Nights and it'd be great if we were able to help each other out some.
key cards for Agency, Syndicate, Miskatonic and Shub
Welcome to the game. I just noticed your post and I will take a stab at this over the weekend. Look for an update soon... 
You can check all the APs by searching here: http://cthulhu.dbler.com/
Disclaimer: These suggestions are limited to the factions you mentioned and neutral cards that would be useful for your decks:
Core Set: Getting multiples of the Core cards is important for deck constancy. There are many cards in the Core that remain staples in the factions you are playing. An alternative to buying more sets of the Core is to find people on the Trade Forum who are getting rid of their CCG cards and filling your set in with the black boarder versions. The only issue with this strategy is the backs are different so you will need to put opaque plastics on your cards. If you go this route I can give you a list of must have more than x1 of Core cards.
Secrets of Arkham: You get x2 of everything and there is nothing that is a must have x3 for any of the factions you are playing. The few cards that would be nice to have a 3rd of you can get by acquiring ccg cards as mentioned above.
Spawn of the Sleeper: There are 2 MU cards that are really top notch in this AP. Unfortunately these choice cards only come x1 and this is a hard one to find. I might be able to help you out on this one if you cannot find it anywhere because I picked up an extra SptS AP in anticipation of need.
Horror Beneath the Surface: lots of good stuff across your Factions so I would make this a priority buy. At least x1.
Antediluvian Dreams: Great stuff for Shub and a solid Agency Support Card. Getting x1 should work.
The Path to Y'ha-nthlei: It has Hired Muscle for Syndicate but somewhat minor buy for other factions. You only need x1 of this.
In Memory of Day: great cards for Agency and MU. You only need x1 of this.
Sleep of he Dead: Several interesting cards. Agency event Behind Bars is great, Syndicate character Clover Club Executive is awesome but he only comes x1 so if you get it you will want multiples of this AP.
The Yuggoth Contract Cycle, Includes: Whispers in the Dark, Murmurs of Evil, The Spoken Covenant, The Wailer Below, Scream from Within. These come with x3 of everything and all have some love for the factions you play. These are universally the best buy APs and I would make sure to pick x1 of these as the highest priority. Of these Murmurs of Evil is perhaps a bit less necessary than the others.
The are others good APs that I did not mention but, given your faction preferences, I tried to stick to the ones most advantageous to making better decks. Of course these are just my opinions and you may like some cards I am not wild about… At any rate, I hope this helps!
Thank you so much! I will look at these!