Each one is fine in a certain context.
If, for example, you want to answer the question,
"Where have you worked in the last five years?" you might respond, "I have worked [here at ABC Company] for five years."
If you want to answer the question
"At what point did you switch jobs in 2001?" you might respond, "Well, I had worked at ABC Company for five years when I decided to move to Yemen, where I then worked for DEF Company from 2001 until 2009."
Notice you followed up "had worked" with a job that took place AFTER that job was completed.
If you want to answer the question
"Where did you work since 2008?" you might respond, "I worked [here at ABC Company] for five years."
The verbs used, from examples one to three, respectively, are: present perfect tense, past perfect tense, and simple past tense. See http://www.youtube.com/watch?v=_8ObuO5neR0 for a nice video on the differences between the present perfect and the past perfect tenses.