If you create MSI setups with WiX Toolkit you should be aware that <icon /> tags in your .WXS file will cause your resulting MSI file to grow by the size of EXE file linked in SourceFile attribute.
Don't do this:
<icon id="example.ico" sourcefile="SourceDir\MyApp.EXE" />
Always use small .ICO files.
<icon id="example.ico" sourcefile="SourceDir\MyApp.ICO" />
If you don't have the icon files you can extract them from the MyApp.EXE binary by running an icon extractor. Just search on the net, there are many free tools available like IconExtract.