Certainly. You can run BW without R/3 implementation. You can use pre-defined business content in BW using your non-SAP data. Here you simply need to map the transfer structures associated with BW data sources (InfoCubes, ODS tables) to the inbound data files or use 3rd part tool to connect your flat files and other data sources and load data in BW. Several third party ETL products such as Acta, Infomatica, DataStage and others will have been certified to load data in BW.