Encoding algorithms better than or equivalent to Run Length Encoding
There are many general-purpose compression algorithms, for example Lempel-Ziv and its many variants (used for example by gzip), and Burrows-Wheeler (used for example by bzip2). You can just try them on your input and see how well they perform. If your data has particular structure, then it is possible that a dedicated compression algorithm would perform significantly better, but it's hard to tell without knowing more about the structure.