One method I've used for sending messages to groups of players on Roll20 is making each group a character and sending a message to that character. Forgive me using a fantasy example, but that's where my experience lies:
At the start of a campaign, I'll ask everyone for languages known, looking for ones I know will come up during play. If anyone knows one, say Elven, I create another character in the Journal simply named Elven, and add every player whose character knows Elven as controlling that character.
When anyone (PC or NPC) speaks in Elven, they can just send a whisper to that group: "/w Elven message" and every player who understands Elven will receive it.
Is there a better option?
To be fair, you mention in the question maybe using Skype instead. Skype can save groups of participants under custom names and be quickly selected from a list. It's a really good idea.
Pros of using Roll20 over Skype:
- The chat history saves everything in a single place, so you can review it easily instead of searching multiple Skype groups for what was said.
- No switching programs, you're using Roll20 for everything.
- You can add an avatar for each group that makes it instantly recognizable.
- You can have "spies" - the GM can add someone to a group, and so long as they never speak to that group, they can listen to everything said in that group with no one else knowing. Excellent in a political game for groups without explicitly declared membership - Illuminati, anyone?
Pros of Skype over Roll20:
- Ease of use: Your players are probably much more familiar with Skype's "click the group, type away" format than Roll20's "/w GroupName message" before every line, especially considering...
- Group identification: When you message a group in Roll20, it doesn't say on the receivers' side WHICH group got the message. So you'll need to train your players to get used to writing "/w NATO (NATO) message", so the people receiving the message know which group they're hearing it in. In Skype, the group is obvious.
- Group-by-group voice chat: Not sure it's a thing for your players, but if it is, Skype offers an easy one-click solution to start a voice chat with a given group.
In the end, which option depends on your group and what works best for you.