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I use KOReader occasionally for PDF files. For ePubs, I find Kobo's renderers work well enough for me. If/when KOReader gets a better metadata search, I may reconsider this decision.
Now calibre? That is a must have software for me. When I first started collecting ebooks, I kept them in a directory structure. Once I had more than ~200 ebooks, trying to use a directory structure ended up with me spending more time modifying the directory structure to allow easily finding a book than actually reading. Then I found calibre. Copy your files into it's library, edit the metadata, covers, etc. and find books based on almost any searchable field including the Full Text Search on every indexable book in your library. calibre and a Kobo ereader go together extremely well including the capability of backing up your device databases and configuration on connecting to calibre. Sheesh... I'm sounding like a fundamentalist...
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