I'm not sure if this project has been abandoned, or if it's just considered to be good enough to not need changes over the past three years. If it's not abandoned, I have a suggestion.
The Base64DecodeReplace and Base64EncodeReplace services would be much more seamless if they didn't visibly launch the Base64Anywhere application, but instead simply replaced the selected text. If the current behavior is intentional, then a way to toggle the behavior would be very useful. I may make this change myself and submit a pull request, but I probably won't bother doing that if the project is abandoned.