The following enumeration is from the cc65 mailing list. The order implies no judgement, it's alphabetically. Feel free to correct entries or add to it as appropriate. The programs should be available to the general public, so while it's nice if you compile all your programs with cc65, this is not the place to list them if they're private.
A2Command is a filebrowser based on CBM Command running on Apple //e, //c, IIgs.
Breadbox64 is a twitter client for the C64 that runs on Contiki. The source is available in the Contiki Projects Community.
Cbmsh is a unix-like shell for 6502 based commodore computers. The source is available at www.opbyte.it.
C-Vote is “a computerized voting system for demo parties that runs on C64:s. Of course it's not only limited to demo competitions, and the code is easy to port to other 6502-based platforms supported by the cc65 compiler.” (source included)
CBM Command is a filebrowser running on C64/C128/VIC20/PET.
The Contiki OS, originally developed by Adam Dunkels was first written using cc65. It has been improved since then and ported to many more platforms. Although today it's focus is on embedded devices a few enthusiasts maintain a version that does still run on 6502 platforms.
Contiki BBS is a contiki based telnet server for the C64. The source is available in the Contiki Projects Community.
Timo has written a tool named FM Radio for C64 to listen to the radio.
GuruTerm is a commodore graphics enabled telnet client for the C64 written in assembler and C.
rt65 is a preemptive multitasking kernel/OS written mostly in C with minimal use of assembler.
Serial Slave is “is a system that allows you to use a PC as a virtual disk drive for your C64 or C128. It communicates using RS-232 and doesn't require any custom hardware. The PC server also runs well under multitasking operating systems, so you don't have to dedicate a machine to running Serial Slave. Serial Slave is fast: 3.8 kB/s with a SwiftLink, 11.5 kB/s with a Turbo232 or Silver Surfer, and even 23 kB/s with a SuperCPU if your PC supports 230400 baud.” (source included)
Alter Ego is a puzzle platformer for the NES written in C/assembler. (source included)
CardSwipe is a card game for the C64.
Clone of the flash puzzle game 'Znax' with improved score system for Atari-8-Bit computers. The 'plus' version has minor fixes, is NTSC compatible and supports Atari CX77 touch tablet or similar devices (CMI08 PS/2 mouse interface).
GNU Sudoku is a port of the well known game to the C64.
Remake of Snake Byte by Sirius Software first published in 1982. This for the C64 with a conio port.
The Atari Lynx Solitaire (source included) contains three games:
The Potion is a text adventure for the C64 written in C/assembler. (source included)
UWOL - Quest for Money is a jump'n'run game written in C and Assembler, ported from the Spectrum version.
Wumpus 65 is a text adventure written in C. runs on C64/C128/plus4/pet. (source included)
The C64 game Zoo Mania was written in C/assembler. (source included)
BCC #3 Party Scroller is a C64 demo by C64 club berlin. (source included)
Bunkerparty 2008 Invitation is a C64 demo by Dienstagstreff.
MatrixCevi is a simple “matrix” effect for the C64 written in C. (source included)
Minicast is an interactive raycasting demo for the C64 written in C which makes extensive use of inline assembly. (source included)
Se gitai o Ilios is a C64 demo by Cascade. (source included)
The 1.x firmware of the 1541 Ultimate uses cc65 to build the menu program, which is written in C.
The boot loader and menu program of the Chameleon are written using a combination of assembler and C.
Chip-8 Emulator is a Chip-8 Emulator for the C64 written in C and assembler.
Eliza 65 is a port of the well known Eliza program. (source included)
pico]OS for 6502 is a realtime operating system by Dennis Kuschel. (source included)
No, the famous Commodore emulator VICE was not compiled with cc65 But some of the test programs are, as Marco van den Heuvel writes on the mailing list:
The joystick (including userport) test-program(s) in the VICE testprogs directory of the svn is done using cc65 (source included).