One of my companies is a distributed company, so we don’t share the same physical space. Our brainstorm meetings are organised via Google Hangouts. One of us (team leader) shares his screen and we work on the same project. The project contains a list of tasks (ideas) which the team leader analyses one by one. Everyone can, at any time, add comments, populate custom fields, new tasks, but it is the team leader that manages the organisation of the project.
In this way we start from the ideas which are not yet organised and understand their feasibility, priority and so on. When no new ideas are in the project, we start going back to old ideas, check if any of them needs to be re-discussed, which ones are ready to be worked on and which ones need a different prioritisation.
The project is always available, even outside the meeting, so that everyone can add or update the ideas.
The challenge is keeping people motivated while they sit alone in front of a computer, more than together in a room.