One small issue I've always had with Blender was it's color scheme. 90% of it is fine, but there are a few elements that slowly give me a headache the more I look at them. The vertices colors - that mixture of pink and yellow - there's just something wrong with it, especially after a few hours in front of the 'puter building a model. And the default color for selected objects in object mode is similar.
It was only a few months ago [when I started getting serious about learning Blender] that I discovered the hidden user defaults [aka. application preferences] which live above the main menu. Yep...that's right - above. The main menu is a window which can be dragged down to reveal a whole new world of options. And one of the options available is Themes.
There are only two themes available after you install Blender, but in the great tradition of making 3D application UIs as flexible as possible, Blender hasn't let us down. You can create your own themes and modify the colors of almost everything you see. And then by pressing CTRL + U, save the them as defaults.
Apart from the themes, there are a lot of options to be found in the 'hidden' user preferences. View Controls [Grid Snapping, Menu Auto Open, View Rotation, etc], Edit Methods [Mesh Undo Level, Auto Keyframe On, Duplicate with Object], Language & Font, Auto-Save, System & OpenGL settings, and Default File Paths. After making changes, you need to press CTRL + U to save the changes. Doing this creates a file called .B.blend in your home directory, allowing you to upgrade without loosing your defaults.
Like I said, I found the user preferences menu a while ago, but the CRTL + U part is vital, otherwise you're changes get lost when you close the app. This I only discovered today when I was fooling around with the Themes. Now I have a Blender with the colors I want. When I open Blender, I get the 4 3D views I like to use. I can finally start organising my supporting files [scripts, textures, sounds] and rendering locations. I'm having one of those Blender moments when you realise just how lucky we are to have such a powerful and professional application available to us. Of all the great 'large-scale' open source projects [eg. Linux, Apache, MySQL, to name a few of the many], Blender has to be up there with the best of them. I'm stoked.