File Splitter - Utility with GUI for splitting files to any size you specify. [Open source] - http://www.examsguide.com/opensource/inoursite.html
JarScan - Searches through archive files for class files. [Freeware] - http://www.inetfeedback.com/jarscan/
DynamicPDF Merger for Java - Allows merging, stamping, appending, form filling and page placing, rotating, scaling and adding new content to existing PDF documents. [Shareware] - http://www.cete.com/Products/MergerForJava/
Jcrontab - A scheduler written in Java. Reads and stores the tasks to execute in a file, a data base or an EJB and provides a web basic UI. [Open source, LGPL] - http://jcrontab.sourceforge.net/index.shtml
Fsgrep - A simple Java application which allows a user to search all files in a directory structure for lines matching a given pattern. Its functionality is like a combination of the Unix 'find' and 'grep' utilities, but with more features. [Open source, GPL] - http://fsgrep.sourceforge.net/
JavaDiff - A command-line utility for reporting the differences between ASCII or binary files, or recursively finding the differences between two directories. [Freeware] - http://www.launchsoftware.com/A555F9/jj2.nsf/displayall/JavaDiff_11.htm
jDictionary - Translates words and phrases from one language to another. Includes pluggable dictionaries and lexicons. [LGPL] - http://jdictionary.sourceforge.net/
JPassGen - A strong password generator for secure login protection. [Open source, GPL] - http://jpassgen.sourceforge.net/
Java Time Calculator - Simple program for calculating time intervals; can be particularly useful to pack audio tracks on magnetic tapes or disks. Can be run as applet or application. [Open Source, GPL] - http://sourceforge.net/projects/timecalc/
Jacksum - A checksum utility entirely written in Java (JAva ChecKSUM). It supports most common checksum algorithms (Adler32, BSD sum, POSIX cksum, CRC-16, CRC-32, MD2, MD5, SHA and Unix System V sum). [Open source, GPL] - http://www.jonelo.de/java/jacksum/
Java Console - A powerful Java Console Client written 100% in java. Mainly written for System Administrators, Coders and also written with the intention to be plugged into various other applications. - http://javaconsole.sourceforge.net/
Follow - Allows a user to monitor several log files concurrently. [Open Source, GPL] - http://follow.sourceforge.net/
jGoodies - Includes jDiskReport, a free cross-platform graphical disks report utility. [Freeware] - http://www.jgoodies.com/
jTask - GUI-based Task Scheduler for Java classes. [Free for non-commercial] - http://www.branchcut.com/jTask/
Java Tar - Tar archive handler creates, lists, and extracts TAR files. Supports gzipped tar files. Can be invoked either using its Java API, or from the command line, or from a GUI version. [Open Source, GPL] - http://www.trustice.com/java/tar/
Diff - Port of Diff, a program to print out differences between files, to Java. [Open Source, GPL] - http://www.darwinsys.com/freeware/Diff.java