Still my favorite refactoring tool is good ol' EditPlus in combination with Total Commander's super fast file search. (Hint: Alt+F7) I totally agree with Mark Biek's reply that you want to have full control over what is replaced where and when.
Whenever i have to do a some refactoring, i create a list in total commander of the files i want to alter by either searching with the built-in function or just by selecting them, and then i drag them all to EditPlus
Editplus can search & replace through the current file, a selection or all opened files using normal text matching, regex matching or multiline matching. It really gives you full control :)
Also, what comes in handy for code refactoring is EditPlus's Macro Recorder (Ctrl + Q to start recording macro 1-9 and Alt + 1-9 to playback a macro).
Once you get the hang of it, you know you can just search for a variable, ctrl + shift + (home || end || arrow keys) through your code, delete, copy/paste and use al that keyboard wizardry to like, for instance, convert a CSV file into a bunch of SQL queries within 30 seconds.