I've only ever used cut-n-pastse, but there are a few things that will help:
Try to keep your line-length down at 70 or so, if possible. The <code> tag will handle clean wrapping of the lines for display, but that will reduce the wrapping, which will be easier to read.
Using tool-of-choice, expand tabs out before copying into the paste-buffer. Depending on how the application (xterm, kterm, xemacs, etc.) interacts with your windowing environment, it may or may not do that automatically.