I have been working on some Domino Cubes and have learned quite a lot about glue joints by asking around to try to strengthen some of the weaker joints in this particular puzzle. I got most of the info below from John, Robert, and Tom Lensch. I am merely summarizing so it is all in one place we can refer to later if needed. Maybe this is all old news...
The troublesome joints in the Domino Cube are the ones where one domino butts into the side of another - forming an end grain to side grain joint. This is also a small glue joint, only 3/8" x 3/4" for the dominoes I have been using. Taking into account the suggestions of the others, I have started producing acceptably strong joints. If you have a similar problem, you might try some of the observations form below - set up somewhat like a checklist.
1. Make sure the pieces fit snugly together without any gaps (even tiny gaps). Sounds easy, but when I got rolling, there was a tiny internal gap that I didn't see - and this also happened to be an end-side grain joint. We all know the PVA (polyvinylacetate - yellow glue) glues don't work well to fill a gap.
2. Suggestion from Robert: On the end grain especially and maybe also on the side grain, cut small incisions in a criss-cross pattern. This allows the glue to get down in the end grain and better bond the joint. Of course end grain on some woods can draw in the glue, so a second application may be needed right before you put the pieces together. Tom suggested rubbing the pieces together, then taking them apart, applying glue to the end grain the second time, then putting them in position to set.
3. If possible, leave a couple pieces unglued at the troublesome joints for the first round of glue-up. This may allow the puzzle to come apart without force the first time - which may give an opportunity to make sure everything slides easily (adapted suggestion from Tom). If there are pieces that fit too tightly, these could be sanded down a little (if you plan it right) before the final glue-up.
I tend to make cubes very tight fitting - a habit I formed from making Convolution and Involute puzzles where all of the joints are very visible on the outside (not obscured by cmamfers, etc). I usually do this using a square corner jig to build the pile of pieces into a cube with glue in all the right places, then clamping it tight from all 3 directions. This turned out to be my own nemisis on the Domino Cube - since the pieces fit so tight that I almost always break the weak joints the first time I try to take the puzzle apart.
4. Suggestion from John: After the final glue-up and all the joints survive the first disassembly, I have started to take a little bit of thin CA (cyanoacrylate - "super glue" - but use a good quality CA) and get it to seep down into the joint to reinforce the PVA glue joint. If there is a tiny gap left, this may assist in strengthening the joint since the PVA will be weak with a gap.
5. If all that still fails - clean all the glue off the joint and try a 2-part epoxy on the failed joint. Try to expose clean wood fibers if possible, and maybe cut new incisions before applying the epoxy.
I have read other techniques including the following
Making small sockets inside the joint and filling with thick CA or Gorilla glue
Gorilla glue foams during curing, which can glue the whole works together - so beware of that.
Any other ideas, please add! I hope this might be useful to someone.
Thanks to all for the help!