How can you represent good tradecraft in GUMSHOE-based games, such as Esoterrorists? That is, the techniques used in espionage, the topics or techniques (dead drops, for example).
Here are some suggestions. I'll assume a modern setting. I think The Esoterrorists is your closest fit, so let's go from there.
Remember to always think in terms of getting clues. For example, if you're wondering how to implement a Dead Drop, think how you'd use a Dead Drop to get clues. (Often, you will find that tradecraft considers techniques for passing on information, whereas, for GUMSHOE, you must consider receiving information).
With that in mind...
Make it so you use Investigative Abilities for uncovering clues, General Abilities for other stuff. This sounds obvious, but the problem is: many tradecraft skills, such as Shadowing (Trail of Cthulhu) and Surveillance (Esoterrorists), are currently general abilities. Since they will be used mainly for getting clues, try making them into Investigative Abilities.
So, in your Dead Drop example, we could upgrade Stealth to an Investigative Ability, then spend a point to get the clue from the dead drop. Similarly, if tailing someone in a car, we might upgrade Driving to an Investigative Ability, then spend a point to find out where the car is going.
(Note: you can, in any GUMSHOE system, spend a point of a General Ability to get a clue. However, if the abilities are primarily used as Investigative Abilities, we should reclassify them.)
Use existing abilities where possible, even if you need to import them from another system. For example, Locksmith is a Trail of Cthulhu ability, but it's not usually used in Esoterrorists. However, it's great for spy stuff. So import it into your game.
So, to take an example of searching someone's apartment for a clue: you spend Locksmith to get the clue from their apartment.
Use Interpersonal abilities for all aspects of Tradecraft that involve interacting with people. For example, to recruit someone under a false flag, you might use Reassurance or Intimidation (depending on how you want to do it).
Split abilities if you need to. An unwritten rule of GUMSHOE is that, when you need more specialised skills, you can split them. So, for example, you could split Electronic Surveillance into Bugging and Radio Surveillance.
Add new abilities if you're covering new areas, but keep them close to existing abilities. For example, you might want a Seduction ability for honey traps. This doesn't really play a part in Esoterrorists or Trail, but it'd fit nicely in a spy game. So create one, but make it work like Reassurance or Intimidation.
Overall, I think you've got most of the tools you need, especially if you scour the different systems. Where possible, use what's there; where it's not, stretch the existing system.
Some more specific examples, using the above techniques. All of these are either Investigative Abilities or General Abilities used as Investigative Abilities: that is, for all of them, spend a point rather than making a roll.
And so on.
By the way, I showed this question to Simon (who publishes GUMSHOE) last night, and he said that Night's Black Agents will answer most of these questions when it's released. So there you go.
Much of tradecraft isn't easily simulated by a roll, so much as player knowledge. Clandestine HUMINT techniques are a function less of unique skills and more a function of knowledge of how to apply said skills.
For example, in Esoterrorists, we have the Cryptography skill which covers many of the crypto functions of tradecraft, and should be extended to preparing messages for passage. Especially as the skill, in a forensic sense, is more cryptanalysis than cryptography, letting players know that it is allowed in both senses seems workable.
Evidence collection, with training in tradecraft, also suggests finding evidence of dead drops, and other forensic counter-intelligence investigations. Photography used to be vital, as many techniques aren't good at passing bulky papers, requiring that written notes be turned into microfiche.
Streetwise could be used to spot tails, perhaps even to do a brush-pass. And so on and so forth. While there could be a "tradecraft" skill, the skill would be more of a planning nature as the actual execution of these practices are well covered under other skills.
If your players are unfamiliar with intelligence and counter-intelligence, a cheat-sheet or link to Wikipedia would be appropriate, so they know what actions are feasible in the game.
I have to agree with @BrianBallsunStanton, tradecraft in general might be an acceptable skill for some games but not GUMSHOE which has very fine grained ones. I agree with his take that it's mostly covered and to "tell them what they can do" - and you may want to flesh out the skills list in weak areas important to you.
In fact, it seems like the biggest gap is that the skills as described are almost completely reactive. In the default investigative paradigm of the game the skills are usually used to "find a clue" or "get him to tell you" not "plant false info" or "turn an asset." But that I think is as simple as resetting expectations, and between all the interpersonal skills and Crypto I think the vast majority of tradecraft is already represented.
If you want to track cover identities and safe houses and that kind of stuff, then I think like in the "relationship with organizations" question you'd add a separate "skill" (really just a point pool) called "Cover" that would reflect the remaining utility of the PCs' resources in that vein.