I usually choose the "Replace with" option, then use find and replace
to clean up any remaining oddities. A character that normally wouldn't
appear in your document (such as ^ or %) makes a good replacement.
Tip: If you save your document before using the Zap command, it's easy
to tell if any gremlins were present, because the black dot will only
appear in the toolbar (and/or the window's red close box) if the
document has changed since the last save. No dot, no gremlins (hence
nothing to find and clean up).
If your need for replacing non-ASCII characters is more advanced, the
Grep section in TextWrangler's Help includes info on matching
hexadecimal characters.