JIRA is perfect for this, we have been doing this for quite a while. Here it goes:
We have created a issue type "Absence".
A field "Type of absence" has values like "Regular vacation", "Flextime", "Other" (e.g. Illness).
Than we have two fields "Start Date" and "End Date" which are mandatory.
An employee creates a absence issue. The absence workflow gives him the opportunity to pass it to his manager for approval. After this it goes to a state "Absence Planned". So an employee can create his absences, each for one vacation, early in the year.
When an employee is going to holiday, he sets the status "Absent".
After this the transition "Back again" closes the issue.
For an overview I created a dashboard with an list of all open issues that have the type absence. As Start and End Date are Fields you can have a nice list in the way:
Markus Absence Planned 10/10/15 10/15/15
Paul Absent 07/20/15 07/25/15
Hope that helps!
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