Set files to read-only : Works for now, Badspot has hinted at it causing issues in the future.
GUI Replacer : I don't think it even works anymore.
User Content Alpha: No longer supported, slightly more taxing on harddrive, may not work for all cases.
Custom UI : Can cause lag upon initial opening of certain GUI, incompatible with some neat client-sided mods.
Custom Launcher : You have to know how to do it.
Read-only and custom launcher are probably the best options as of today.