I have tons of sample codes written in Shift-JIS with line endings of CR/LF (Windows). Below is an AppleScript to convert such documents to UTF-* encoding with LF (Unix). I use CotEditor because its encoding detection works better (for me) than BBEdit.
tell application "CotEditor"
activate
set properties of document 1 to {line ending:LF}
convert document 1 to "Unicode (UTF-8)" with lossy
-- Use regular expressions to replace yen symbol with backslash
replace document 1 for "\x{00a5}" to "\\" with RE and all
end tell