When deciding what document format you choose, you should make sure that team members (or are you working alone?) are comfortable working with the format itself.
Storage is not so much the problem as is being able to see diffs between versions and merging. In my experience, nothing beats text formats that can be edited freely in any text editor. This excludes HTML and about any XML-based format. DocBook being a barely usable exception.
A good wiki that can use any of the popular version control systems and be set up in a distributed fashion is IkiWiki. With IkiWiki, markup parsing is done in plug-ins, so you can choose input format on a per-document basis. The "default", Markdown gets pretty close to plain-text formats.
If you're unhappy with using LaTeX, don't use it. I think it's unsuitable for taking quick notes. Man pages are written in nroff, but many people use other formats such as POD.
Some projects that strive to be alternatives to Visio are Kivio (KDE) and Dia (Gtk/Gnome). I haven't used Visio itself, so I can't comment on their feature sets. It probably depends on what sorts of visuals / diagrams you want to create. UML? Flow charts?
