There is not one "best" way to do this.
- Tom Kyte uses a package called "debug".
- Steve Feuerstein uses a package called "p".
- I use my own package called "DPS". http://www.oracle-base.com/dba/miscellaneous/dsp.pks http://www.oracle-base.com/dba/miscellaneous/dsp.pkb
- There is a project called log4plsql, similar to the Apache log4j project.
You should play around with them and see which you prefer.