I use NERDTree and quite like it, but I never keep it open. I have :NERDTreeToggle mapped to <Leader>f, so if I need to open a file I can quickly press `,f`, find the file and then press `,f` to close NERDTree. One thing I find annoying about this is that in MacVim, NERDTree creates a scrollbar in the left hand side of the window that I can never seem to get rid of.

Once the files are open, I tend to use buffers, splits and tabs to navigate between them. NERDTree is just used to load a file into a Vim buffer. Also note that the NERDTree explorer replaces the default vim file explorer.

I heard good things about Command-T though, maybe I'll try that and see if it works better with my workflow than NERDTree.