It is possible to customize the customer portal with custom HTML (additional informations, links to other applications and wrote more introducing help texts)?
Not possible at the moment. You might want to raise a feature request for that.
Possible alternatives include:
Please refer to the portal documentation for more tips: Customer Portal Best Practices
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Service desk for Service Pack has many feature for JIRA service desk and there is option like add links. You can link it to other application and it will be shown on top of the SD.
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