On the number of column families
HBase currently does not do well with anything about two or three column families so keep the number of column families in your schema low. Currently, flushing and compactions are done on a per Region basis so if one column family is carrying the bulk of the data bringing on flushes, the adjacent families will also be flushed though the amount of data they carry is small. Compaction is currently triggered by the total number of files under a column family. Its not size based. When many column families the flushing and compaction interaction can make for a bunch of needless i/o loading (To be addressed by changing flushing and compaction to work on a per column family basis).
Try to make do with one column famliy if you can in your schemas. Only introduce a second and third column family in the case where data access is usually column scoped; i.e. you query one column family or the other but usually not both at the one time.
