Here is a list of applications that are currently available on Cydia. Please feel free to add any other app in the comments.

Administration

IOKit Tools – ioalloccount, ioclasscount, ioreg
iPatcher – removes the brick mode from iPhone
Kernal Extension Tools – tools that work with kernal extensions
Isof – shows what files programs have open
Sudo – temporarily assume root priviledges
top – at-a-glance process watching tool

Archiving

cpio – predecessor to tar that is used by RPM
DMG2IMG – converts compressed dmgs to HFS+
fastjar – faster native alternative to Java’s Jar
libarchive – backend library for working with tar files
rzip – the best compression algorithm
unrar – de-compress files in rar format
7-zip (POSIX) – claims to be a good compressor

Data Storage

cvs – the original popular revision control
Git – fast content-addressable filesystem
Subversion – modern version control system

Development

APR – platform abstraction library from Apache
APR-util – data structures and utilites for Apache APR
Assuan – GnuPG’s inter-process communication
Bison – GNU parser generator derived from Yacc
Bootstrap Commands – Mach interface and stub generator
Class Dump – reverse engineer Objective-C headers
Csu – library loading and support stubs
Darwin CC Tools – linker and assembler for the iPhone
developer-cmds – ctags, error, hexdump, rpcgen, unifdef
Flex – GNU lexer derived from Lex
glib – basic object management used by Gnome
GNU C Compiler – a native c compiler _on_ the phone
GNU Multiple Precision – (Big) Arithmetic Library
GNU Portable Threads – portable threading library used by X
Google Data API’s – GData client library (Objective-C)

indent – automatically prettifies a C program
iPhone 2.0 Toolchain – Full *compatibilty toolchain with one click! Use this to compile your 1.1.x apps for 2.0 with some limitations. BigBoss’ headers for 1.1.1 from working Cygwin toolchain. Also depends on all other necessary packages. Copies to /var/include and symlinks /usr/local/include to /var/include if possible. Also links gcc to arm-apple-darwin-gcc.

libffi – dynamic generation of function calls
libgpod – ipod data access library
libsigc++ – callback framework for C++
LibVNCServer – backend library for VNC servers
Link Indenty Editor – pseudo-codesign Mach-O files
Make – dependency-based build environments
Patch – merge a difference onto a file
XML Parser Toolkit – Stream-oriented XML parser written in C

Games

Macman – an outstanding Pacman knock-off with a nice twist!

NES – NES Emulator for iPhone
quake4iphone – Includes shareware Quake files. Retail files highly recommended. Visit zodttd.com for more info.

ScummVM – is a program which allows you to run certain classic graphical point-and-click adventure games, provided you already have their data files.

Java

Classpath – open source implementation of Jave
iPhone/Jave – example applications (with source) in Java
JamVM – Small, intricate, fast Java interpreter
Java SQLite – JNI bindings and JDBC driver for SQLite
Jikes – native faster alternative to Java’s javac
JocStrap – Java/Objective-C connection library
Rhino – Java implementation of Java Script
UICaboodle – iPhone-specific JocStrap extensions

Localization

BrFix – Brazilian Regional Fixes
RuFix – Russian Regional Fixes
Slovak Language Replacement

Multimedia

FAAC – open source library for MPEG-4 AAC
FAAD – open sournce library for MPEG-4 AAC
Festival-Lite – embedded text-to-speech library
LAME – open source (lgpl) mp3 encoder
Ogg – open multimedia container format
png – library for manipulating PNG files
SwapTunes – Allows you to Sync with multiple iTunes libraries.
TIFF – Tagged Image File Format library
Vorbis – Open audio compression format
x264 – open source implementation of x264

Thanks to Cliffeman for compiling this list over at Everything iCafe.