What are different Java APIs to access different file formats ?

MS Access

JDBC/ODBC bridge 

JDBC driver for ODBC databases, comes as part of the JDK; on Linux, you'll have to get ODBC up and running first: http://www.unixodbc.org/

Jackcess 

Library to read and write MDB files

HXTT Access 

Commercial pure Java JDBC driver for MS Access

CGM

cgmva

An applet to display CGM files; comes with source code

CHM

JChm

Library to read CHM files

MS Excel

Apache POI

Library to read and write XLS files

Ostermiller Utils, CSVObjects, CSVBeans, opencsv, Java CSV

Libraries to read and write CSV files. CSV is not as easy to read and write as it first looks - once all the special cases are considered, one might as well use a library.

JExcelAPI

Library to read and write XLS files.

jXLS

Library for writing XLS files based on templates

Java2Excel  

Library for creating Excel files based on Collections. It is possible to use JDBC to read Excel files

Obba  

works with Excel spreadsheets on Windows

OpenXLS 

OpenXLS is the open source version of ExtenXLS - a Java spreadsheet SDK that allows you to read, modify and create Java Excel spreadsheets from your Java applications.

Gedcom

GDBI, GenJ

HDF (Hierarchical Data Format)

Java products by the HDF Group

Images

ImageJ 

Java image processing application and library that has plugins for lots of image file formats

JIMI 

Library to read and write BMP, CUR, GIF, ICO, JPEG, PICT, PNG, PSD, Sun Raster, TGA, TIFF, XBM and XPM. There's a plugin for using JIMI with ImageJ, which also includes a couple of JIMI patches.

GIF write, and TIFF, RAW, PNM and JPEG2000 read/write support for ImageIO

INI

ini4j "is a simple Java API for handling configuration files in Windows .ini format."

Matlab

JMatIO - Matlab's MAT-file I/O in JAVA

OpenDocument (ODF)

basic Java code for reading ODF files is here

ODFDOM 

A Java library for accessing ODF files.

jDocument.org 

has an open-source library for accessing all Open Document file types.

Obba  

works with OpenOffice? spreadsheets

Office2FO 

converts ODF documents to XSL-FO documents, making possible further transformations (like conversion to PDF using FOP)

Office Open XML

These are the new XML-based Microsoft Office formats.

OpenXML4J

ocx4j 

create and edit docx documents using a JAXB content model matching the WordML schema

Apache POI  

implements these formats.

OpenOffice Java API

OpenOffice can read a number of file formats, and makes them accessible through its API. A starting point might be this article, this article and of course the OO developer site

Some introductory information about the OO file format can be found here and here

oooview 

An OO Viewer written in Java.

JODConverter

A Java library that uses the OO Java API to perform document conversions between any formats supported by OO

Outlook

The Apache POI project developed some code that can read the texual contents of Outlook's MSG files. This page talks about that.

Xena  

converts multiple file formats -including MSG- to XML. Either the result of that conversion, or Xena's source code, may be helpful.

JPST  

can read and extract PST files.

PDF

PDF is a hard to read format. 

The best one can do is try to extract the text contained in a PDF file.

iText

Library to create PDFs; see ItextExample for a code example. The older version iText 2 (which uses a more permissive license) is also available: jar file, javadocs

FOP  

Libray to create PDFs (and other formats) from XML by using XSL-FO transformations

FlyingSaucer

Library to convert CSS-styled XHTML to PDF

PDFBox

Library that can merge, split and print PDFs, extract text, create images from PDFs, encrypt/decrypt PDFs, fill in PDF forms and more

PDF Clown  

General-purpose library to read/create/modify PDF files. 

It features a rich multi-layered object model that allows access even to each single content stream instruction.

JPedal

Library for viewing and printing PDFs, can also extract text (how to print PDFs); commercial (the LGPL version provides PDF viewing only)

PDFTextStream

Commercial library to extract text from PDFs

Adobe AcrobatViewer for JavaBean

Freeware, library to display and print PDFs

This library hasn't been updated in a long time and has problems displaying files that were created with recent PDF versions.

Don't use this for anything new.

PDF Renderer  

A more up-to-date PDF viewer that renders using Java2D. Download, Examples, Printing PDFs

ICEPdf  

Another library that can render PDFs.

Qoppa  

offers numerous libraries for PDF-related tasks

Aspose.Pdf  

A commercial library for reading and writing PDFs

MS PowerPoint

The Apache POI project developed some code that can open and (to a limited extent) edit PPT files. This page talks about it.

Project

The MPXJ library can work with several Project file formats.

PST

LibPST 

C library that could be used through JNI.

Xena  

can convert multiple file formats -including PST- to XML. 

Either the result of that conversion, or Xena's source code, may be helpful.

java-libpst  

A pure Java library that can access 64bit PST files.

QIF (used by Microsoft Money and Quicken)

Buddi and Eurobudget are Java applications that can import and export QIF files (and thus contain code you may be able to use in your application). Both are licensed under the GPL.

RTF

jRTF can create RTFs

iText 2 can create RTFs: jar file, javadocs

JavaCC

A lexer/parser for which an RTF grammar is available. From that an RTF reader can be constructed.

MS Visio

The Apache POI project developed some code that can read Visio files.

MS Word

POI  

Library to read and write DOC and DOCX files. It can also be used for extracting the text of a document.

WordApi.exe  

Native Windows component with a Java interface, which lets you create Word documents, and alter word templates. Some impressions about it can be found here.

Something else ?

If you encounter an obscure format for which no library is available, it may be feasible to create a reader for it if you have a file format description (which may be available on Wotsit). 

Several libraries, so-called lexers and parsers, are available that help in creating a reader, especially if the file format is ASCII, and not binary. 

You will need knowledge of regular expressions, though. 

Some file formats that have been tackled using this approach include RTF, CSV, HPGL and PBM/PGM/PPM. Lexers are easier to start with, but parsers can do more of the work for you. 

All these have ready-to-use examples on their web sites.

Lexers : JFlex (introductory article in the JavaRanch Journal)

Parsers : Antlr, SableCC, JavaCC