While working on the gluelogic of my SBC I stumbled upon a very intersting tool called Logisim.
It is able to simulate even complex logical circuits and provides a rich library of basic gates and also some cool features for setting values to single lines or complete busses and display the state of them too.
It is written in java and runs on Linux, Mac OS and Windows without any changes.
From single-line logic circuits you can calculate the truth-table to check if it matches your design.
I've just started to play around with the tool, but it should be perfect to check a gluelogic design in all details.
The picture shows a simulation of Garth's address decoder from the 6502 Primer
The programm is also extendable by building subcircuits you can reuse in more complex circuits. Additionally you can create java classes for special circuits. If somebody takes the time to adopt one of the java 6502 simulator classes to this project you could simulate a complete SBC with RAM, ROM (both already included in the programm in a general way) and a 65(C)02 on a simple hardware layer.

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How should I know what I think, until I hear what I've said.

I also found Logisim a while ago, I was looking for a free logic simulator which would run on Linux. Even I can use it! Which says a lot, I'm normally unable to find my way around the drawing-type GUI tools. My mind doesn't work that way. I had initially tried to use Quartus II in its schematics mode, but I couldn't figure out how to draw a shift register with a method to pre-load it. Anyway, with logisim I was able to 'implement' a circuit from a description of a satellite-specific CRC12 algorithm in hardware (the documentation was simply a drawing of the circuit, plus two lines of text about the initial LFSR value and the final output). This one differs from the normal CRC algorithms in that it has an extra feedback loop which prevents a normal table-based software implementation, so I wanted to 'build' it. It was fun to implement that one in logisim, with LEDs and hex display and input. And pre-loading of the LFSR register. It's not unlike inserting circuits and wires into a breadboard, which means that I can do it. I used the circuit I created to verify my software implementation of the CRC algorithm.
As I said above, I'm not generally good with certain types of GUI tools - I never find what I need where I expect it to be. And that's just one of the problems. Logisim is something I can use though.

Logisim is used in education according to some EDU sites, students have apparently implemented full CPUs in it.

There's a new version in the works btw (under a different name) with some interesting new features.

-Tor