Format for storing textual data
In general, use a storage method that allows you to quickly query it. If your collection is huge, you might need something Lucene-based, like ElasticSearch. If you are a SQL crack and your favorite DB supports it, a full-text index might do the trick. For small sizes like the 5000 documents, even Linux' LocateDb+grep or OSX' spotlight could be enough.

The important point is to be able to quickly verify assumptions about the content of your data - how many documents contain X and Y, does any document contain W but not V, etc.

This will be useful at both the whole set level as well as for analyzing your topic clusters. Finally, a few GNU tools or SQL mastery can also help you profile your document sets more efficiently (n-gram counts/ranks, collocations, concordances, etc)

Edit: that means, for the above reasons and given your collection size, good old plain text (in a file system or a database) might be more efficient than any "fancy" format.