We have a lot of spreadsheets (xls) in our source code repository. These are usually edited with gnumeric or openoffice.org, and are mostly used to populate databases for u
I know several responses have suggested exporting the file to csv or some other text format, and then comparing them. I haven't seen it mentioned specifically, but Beyond Compare 3 has a number of additional file formats that it supports. See Additional File Formats. Using one of the Microsoft Excel File Formats you can easily compare two Excel files without going through the export to another format option.