My js and my markup live together but I still use seperate css. So maybe I was over stating my case but generally, I have a predefined set of styles that I am working from, which means I don't think about the styles too much, other than setting them using classes. I am definitely interested and excited for someone to make an excellent inline styles framework though, but I haven't found one yet.
Currently for most of my projects I still use bootstrap (with a theme or something) and just include one compiled css file and bootstrap.js in my main index (everything else gets put together into one javascript file by browserify). I choose my markup with classes (className) and use bootstraps interactive pieces (accordians, modals, messages) with the markup data api.
If you are really curious, here is a template app I often use to start from. (https://github.com/availabs/dashboardTemplate)