Motherboard:

Because this board has a lot of hardware packed relatively tightly onto it, because it includes a few relatively exotic ICs which only exist as SMDs, and because of the size restrictions of the Light version of Eagle, this board is designed almost entirely around surface-mount components.

Output Daughterboard:

This board contains the transistors for the open-collector transistor outputs (three of them), plus the amplifier and filter circuit for the analog waveform generator output.

Because this board does not contain any particularly specialised ICs, and it does not require so many components packed on with such a high density, through-hole components are used. Some people prefer through-hole components, and using through-hole components on this board means that it is more familar to construct for people who are not used to working with surface mount components, and this means that this project includes both surface-mount components (on the motherboard), and through-hole components on this daughterboard.

Pushbutton keypad board:

The pushbutton keypad is on its own separate small PCB. This makes it much easier to wire up the switches, compared to wiring up individual buttons manually. This simple board includes the six pushbuttons and a string of resistors, and it is designed to be connected to a single analog input on the AVR and the button states read by reading the analog voltage.

This is a very simple board which could easily be constructed by anyone, it is single sided, and the PCB is so simple that it could probably be fabricated at home. It's probably quite valuable as a general pushbutton interface board for general Arduino activities outside the context of the ArduinoLab project, and this board probably has wider appeal for these reasons.

I have written up the BOM for this board in a more verbose format, translating the Eagle-generated BOM into Digi-Key and element14 part numbers, so you can easily go shopping for components. I have not yet been through this for the other boards.