If you are storing blobs such as images then don't use tokudb. It has a smaller row size limit.
If you have data that's over 100 million rows, use tokudb.
If you are sensitive to UPDATE speed, don't use tokudb. It has very fast insert but as compared to innodb, slower UPDATE speed and especially if you use INSERT ON DUPLICATE statements.
If you are storing log entries, use tokudb.
If you want to shrink your myisam/innnodb's data usage by more than 5x, then use tokudb. I have personally confirmed that their fractal tree + compression data backend is extremely space efficient.
Rule of thumb, use the best tool for the job. Tokudb blows innodb and myisam out of the waters in specific situations but is not a general replacement db engine for everything under the sky.