Disclaimer: I don't like mind-maps, they don't work for me. If you want a strictly visual answer this won't be for you.
I run my games entirely from OneNote but this approach should work for most notetaking apps, campaign management tools or wikis. My notes consist of sections for lore, PCs, NPCs, locations, rules (and house-rules), items, and session running notes.
Anything in my game that is important enough to get a name is important enough to get a page or paragraph somewhere in my notebook. Having a page or paragaph means they can be linked to from other pages. Use of links between related entities is at the core of how I handle factions and the like in my games. Each faction also has notes of their motivations and goals to help me decide when interactions would impact them.
Depending on what the factions are they will have an entry in NPCs (possibly multiple), lore and a link from the locations where they exist. On the main faction page I have a list of relations to other factions they interact with. Here is an example of what a faction looks like in my notes:
The Rusted Chain
The Rusted Chain are a heretical off-shoot of the religion known as The Chain. They survive as a group of mercenaries and assassins for hire, only their most devout followers observe the religious beliefs of their origins.
The Rusted Chain is mostly motivated by greed, both for money and power. But their leader is fanatical and believes in stamping out other religions.
- The Chain: Members of the chain despise The Rusted Chain and decry them and anyone associated with them as heritics.
- The Watch: The watch see the rusted chain as troublemakers and won't tolerate them in town. Anyone that is know to associate with them will be poorly regraded by the watch.
- The Merchant Guild: Members of the merchant guild see the Rusted Chain as a useful resource and dangerous ally though are wary of showing it opening lest they bring the wrath of the watch.
In the example above any text that is in italics is a link to the faction page for that faction. By using free text fields I can be as detailed or as sparse as I need to in explaining the relationships.
Anytime my players interact with a faction I quickly check that factions relationship list and make a note on the related faction if it would impact on their behaviour. By not bothering to explicitly write what their corresponding action is I can respond more naturally by reviewing how the information interacts with that factions motivations. In some cases it will simply impact the conversation between the players and the faction, in others they will actually see activity as the result of it.
This system works for items where I have a list of factions/NPCs interested in the item that might come after the party or offer to buy it. It works for individually, factions and entire diplomatic regions. It's simple and quick and doesn't require me to follow any diagrams just click a link in my notes.