We use a combination of an internal wiki and formal documentation (our software is used to collect data during clinical drug trials for new drug applications, s

We use a combination of an internal wiki and formal documentation (our software is used to collect data during clinical drug trials for new drug applications, so certain FDA rules apply to our processes). Currently, the formal documentation is made up of Word documents (no, really) that are managed via projects in Team Foundation Server. We are currently moving in the direction of using JSDoc on our latest project (since it is entirely written in JavaScript), and we will likely have our internal auditors sign off on the format for use as our software design docs.