Everyone does virtual differently. Having worked in bricks-and-mortar previously, setting up a virtual work system as been something of a mix of experimentation with solutions recommended by others. Here are some of the ways we manage as a virtual company.
Email is a place to lose things. We don't depend upon email for critical project communications. We have our own Open Atrium intranet
set up for all of our clients. Here we post research documents, wireframes, flow charts, use cases, design mockups, questions, general messages, and the ever essential support tickets. Our clients can post, comment on and otherwise interact with all of these items, and all the archives are there for review later. No spam filters or non-inbox-zero obstacles!