Not looking to for interface design tools, more a tool to document systems, methods, functions, relationships, etc. Never used anything like UML, but if that's your suggestion, please point me in the direction of a way to rapidly start using it in a way that does not take a month to deploy, and 2-5 days to train others on.
UML apps only take about 15 minutes to install max. It doesn't take months to deploy. There is a slight learning curve, but there's a reason why UML's the standard way to model software systems. If there were anything that could do what UML does while requiring no time to learn, then nobody would use UML.
That said, there are some experimental thought-diagramming/mind-mapping tools that don't have so much structure and thus take less time to learn. One that I've tried is Compendium, but it's not very polished and has some major bugs (like crashing when using parts of the demo project).
Otherwise, you could do what many software developers are doing these days and just diagram workflows/processes (i.e. a flowchart of wireframes). It's argued that this is a better way of designing software (by first designing the interface) than focusing on features. Workflows are user- and goal-oriented. It puts the UI center stage and lets you define the functionality of the app in terms of how users will interact with the site to do what they want. This gets you into a frame of mind that encourages intuitive interfaces and better information architecture.