How can I overwrite a file or prevent 'copy' from being appended?
By default in OS X Mavericks, dragging a file into a folder that contains a file with the same name will prompt you for what you would like to do.

Take, for example, these two folders: Folder1 and Folder2. Both contain a text file called Test.txt.

Dragging Test.txt from Folder1 into Folder2 will result in this dialog:



"Keep Both" will result in the file being named Test copy.txt. "Replace" does exactly what you want - replaces Folder2/Test.txt with Folder1's Test.txt.



As user dval has discovered, earlier versions of OS X may require that you hold down ⌘ while you drag a file into another folder in order to see the "Replace" option.