I suspect I'm in the minority, but I try to use very few frameworks and work my way up as needed.
I've been using Sublime Text 2, and generally developing in Rails + postgresql.
I prefer against CSS frameworks. It's pretty easy to build your own grid system. The exception is that I've been using Bootstrap pretty heavily for new ideas and prototypes, but have also found myself removing it in the long run.
I use jQuery. It works nicely with the idea of using very few frameworks. It's great for DOM, Ajax and events, but doesn't assume too much more. Sometimes I'll use a polyfill shiv of some kind, but usually only when I run into trouble. I don't like heavier frameworks like Ember or even Backbone. Ultimately, I feel like I'm building an Ember app, not a web app, and I think that gets in the way of making good decisions otherwise. Backbone is obviously lighter weight, but I developed a system (patterns) a while back that works really well for me, and haven't found Backbone to be an improvement.
File organization is a really interest topic, and not talked about enough. It's a big one, though, and I think more than I can fit here. Roughly, I have a few "core/setup" files that are included on every page, then the rest of the code broken up into "components" - generally page-specific, and "widgets" things that are likely small in scope, totally independent, and alway capable of having multiple instances. All communication between components, widgets, or any other code is done with custom events.