I'm just gonna drop the obvious Covert Action remake. Really no game like it out there, though Shadows of Doubt seems to be gearing up to provide a spiritually similar experience. Any video game that makes you put together a crazy board is automatically a jam. Thankfully Shadows of Doubt will have it integrated.
The “crazy board” is suboptimal. I used an improvised spreadsheet. =)
Anyway, roughly cut across mini-games, there are 2 parts: stealth and investigation. They are put together because lol James Bond does everything himself, but they don’t really belong together. They’d make more sense as
either playing an operative who runs missions with set objectives
or his commander.
If we are talking free remakes? The stealth part could probably be made in OpenDarkEngine (like Thief series… except mostly with dull architecture).
The investigation part could be made in any non-trivial “script-and-GUI” engine. Not sure about capabilities of ScummVM, but certainly in RenPy (Visual Novel engine), because yet another lump of Python can always be glued to it in a pinch.
To be less of a dry puzzle, it could double as “agent manager” — much like those “sport manager” games, or even Magical Boutique (your component gathering employees have stats that can level up, equipment can adjust those stats, areas where they can be sent have their own parameters, and demand for your products fluctuates wildly). And, of course, Covert Action had minimum of irrelevant activity, but if your world model runs on a modern-ish computer and uses a nice stable backend (maybe even a MySQL database), all other named groups could likewise run operations against you and each other (as the saying goes — there’s plenty more red herring in the sea). Huh. Actually, a “Spymaster” game made like this could be fun (likely approaching ‼FUN‼, in that the opponents should be more aggressive on high difficulty).
Just for some viable baseline:
Stars Without Number has a splatbook
Darkness Visible, which as usual includes a strategy mini-game for dynamic background generation. In this case, the entities are intelligence agencies and secret societies; they have attributes (Connections, Infiltration, Mobility, Muscle, Resources, Security and Tech), Assets (that have levels and increase their attribute by value depending on the level) and current Goals.