You can assign three different waves to every LED. The first two (0 & 1) are 'eternal' waves. They are displayed alternating until anything different is required. The third wave (2) is only displayed once; afterwards the device will switch back to alternating between the first two waves.

They are displayed alternating until anything different is required. The third wave (2) is only displayed once, afterwards the device will switch back to alternating between the first two waves.

One wave is described by three parameters: the waveform, the duration for one repetition of the wave and the number of repetitions before switching to the next wave.

This version supports four LEDs. It should be quite easy to change that number to between one and eight. I have not tested any number greater than four, but I can imagine that the load on the controller may be too high to reliably communicate via USB.

There are three parts included in the distribution: The firmware for an ATmega8 microcontroller, a command line client that can be run under Linux, and the circuits needed to build the device.

This project is based on the PowerSwitch example application by Objective Development. Like that, it uses Objective Development's firmware-only USB driver for Atmel's AVR microcontrollers.

Objective Development's USB driver is a firmware-only implementation of the USB 1.1 standard (low speed device) on cheap single chip microcomputers of Atmel's AVR series, such as the ATtiny2313 or even some of the small 8-pin devices. It implements the standard to the point where useful applications can be implemented. See the file "firmware/usbdrv/usbdrv.h" for features and limitations.
Building and installing

Circuit
The circuit contains only a few standard components. There's no special USB-chip involved.

The installation is described in the documentation.
Usage

Connect the device to the USB port. All LEDs should flash up to indicate that the device is initialized.

Then use the command line client as follows:

usb-led-fader status
usb-led-fader set
usb-led-fader clear
usb-led-fader reset
usb-led-fader show
usb-led-fader test

When using the set function, it is possible to define several waves at once. You simply have to give the parameters for all waves. See examples below.
Parameters

ledId: ID of the LED (0-n, depending on the number of LEDs in your circuit).
waveId: ID of the wave (0-1: constant waves, 2: override).
waveformId: ID of the waveform (0-31: brightness, 32-37: patterns). For a reference to the patterns, use the show function.
periodDuration: Time in sec/10 for one repetition of the waveform. A value of 0 can be used to reset the wave.
repetitionCount: Number of repetitions before switching to the next wave. A value of 0 can be used to repeat this forever.

Examples
Get the status of all LEDs:

usb-led-fader status

This will result in output similar to this:

LED 0 curid curvalue curpos currep nextupd
0 2 26 0 23
wave waveform length repeat duration updtime
0 38 32 1 20 45
1 0 1 1 0 1
2 0 1 1 0 1
LED 1 curid curvalue curpos currep nextupd
0 14 19 0 19
wave waveform length repeat duration updtime
0 38 32 1 20 45
1 0 1 1 0 1
2 0 1 1 0 1
LED 2 curid curvalue curpos currep nextupd
0 31 16 0 43
wave waveform length repeat duration updtime
0 38 32 1 20 45
1 0 1 1 0 1
2 0 1 1 0 1
LED 3 curid curvalue curpos currep nextupd
0 6 9 0 39
wave waveform length repeat duration updtime
0 38 32 1 20 45
1 0 1 1 0 1
2 0 1 1 0 1

In this output, the values curvalue, curpos, nextupd and updtime are for debugging purposes only. They shouldn't be of interest to the common user. The meaning of the other values should be clear.
Set the first LED to keep a moderate brightness:

The device from above
I know that I could have soldered that in a more beautiful way... ;-)

usb-led-fader set 0 0 15 10 1

So, on LED 0 the wave 0 is set to waveform 15. It will stay there for one second and will be repeated once before switching to the next wave. There is no next wave because we didn't define one, so this waveform will stay forever.
Now set a second wave on the first LED, a little brighter than the one before:

usb-led-fader set 0 1 25 10 1

This is wave 1 on LED 0. Waveform 25 has been defined as a constant level of brightness. After setting the second wave, it will alternate with the first one after every second, because both waves have the same duration and the same number of repetitions.
Set a third wave on the first LED:

usb-led-fader set 0 2 36 20 5

This sets the third wave (wave 2) on the first LED. Waveform 36 is a nice sine-like wave, so the LED starts to fade. One period of the fading takes 2 seconds, it is repeated for 5 times. Since this is the third wave, after the repetitions the LED returns to alternating between wave 0 and wave 1, this wave is discarded.
Set multiple waves at once:

usb-led-fader set 0 0 15 10 1 0 1 25 10 1 0 2 36 20 5

This will set all of the above waves at once. Thus, the first LED will first fade the sine-wave five times, then start alternating between the two brightnesses in one-second-rhythm.
Clear the first LED:

usb-led-fader clear 0

This will clear all three waves on the first LED.
Reset the device:

usb-led-fader reset

All LEDs will flash once, to indicate that the device is reset and the LEDs are working.
Show a waveform on the screen:

usb-led-fader show 36

This will lead to an output like the following:

wave 36 - length 64
31: *****
30: *********
29: ***********
28: ***************
27: *****************
26: *******************
25: *******************
24: *********************
23: ***********************
22: *************************
21: *************************
20: ***************************
19: *****************************
18: *****************************
17: *******************************
16: *********************************
15: ***********************************
14: ***********************************
13: *************************************
12: ***************************************
11: ***************************************
10: *****************************************
9: *******************************************
8: *********************************************
7: *********************************************
6: ***********************************************
5: *************************************************
4: *****************************************************
3: *******************************************************
2: ***********************************************************
1: ****************************************************************
================================================================

Keep in mind that the width of the displayed wave corresponds to the length of the waveform. If you display a very simple one like the constant brightness levels (0-31), the length is 1. Therefore only one column is displayed.
Test the device:

usb-led-fader test

This function sends many random numbers to the device. The device returns the packages, and the client looks for differences in the sent and the received numbers.
Drawbacks

As mentioned above, controlling the PWM for several LEDs is a lot of work for one small microcontroller. So is speaking the USB protocol. Together, these result in a lot of load on the device, so the communication with the device is not 100% reliable. More than 99%, though, at least in our tests.