PDF (Portable Document Format)
When used within a database, the PDF Full-Text option will allow users to see an article or resource as it originally appeared on the page. This makes documenting a resource easier as one can easily identify page numbers and sections.
HTML (Hypertext Markup Language)
When used in databases as HTML-Full-Text, the user will receive the text of an article or resource as a block of text. Paragraphs will usually be defined; however, many times pages will not be indicated and images will not be included.
The Verdict:
When you have a choice, choose the PDF format as it will make citing the resource easier.