On Search / Replace I have a small UI/UA concerns. I don't like how the buttons are disabled when in Find Mode and you can't really get to Replace Mode. I liked it much bette when you could do work in modes at the same time. NotTab was great for that. They also had a count occurances check box, but thats a feature and outside the scope of this post.
On Preferences ( this is so minor ) The way the 'Apply' button works is inconsistant with other windows UI's it should stay disabled untill you make another change above.
I am much more concerned with getting out other planned features then nit picking over little things, but I thought I would at least voice it. :)