Homebrew PCBs

I just looked up my email here. The solid beige stuff I bought is 
supposedly CEM1 @.047. The double-sided I was just trying to print on 
is the FR4 and it's .093 (yikes!). Either one seems rigid enough for 
what I'm doing though and everything will likely be supported on 
standoffs or something, especially stuff with controls.

I don't believe either of these has taken toner well, but I can 
probably find a working combo for printing the tops of the flatter 
single-sided etches. I'm looking at a CAT5 tester on that beige stuff 
I built here, which I printed a bunch of junk on and everything stuck 
but one letter. However, that was with Staples paper, so it has that 
nasty gray film on it. I coated it with a spray to darken it some, but 
it's still gray. Wetting that residue makes it a bit better looking, 
but then it dries out. I wonder if there's a paint, etc. that would 
keep it black? Weird thing is, transfers tend to fuse into the PCB 
material unlike the copper, so even the ones that didn't take have a 
leftover ghost if you try to wipe them off.

Sanding or leveling the top with something seems like it may help. A 
lot of mine has that "cloth" texture which probably doesn't encourage 
a good transfer. I don't know if sanding would just bring up more 
cloth though.

Anyone struggling with it may try a light spray before the toner goes 
on. Krylon "crystal clear" acrylic made a world of difference on 
aluminum with the JetPrint paper. It may even take less heat and 
heating time, as it sort of fuses into and "grabs" the toner.

To anyone here- 

Other than the obvious strength and copper thickness or quality 
factors, what exactly should be our concerns with the different types 
of PCB substrate? I'm not in danger of excessive heat either, but I 
don't think I would care for any "warping", etc.

                              -George