I made custom blocks for a resource pack, and used transparent .png created in Paint Tool Sai to make some blocks invisible, and others with only small lines visible. They are properly transparent in 1.7.10 (though you can see through the whole world through the bottom, but that's another issue...).

But in 1.8 and 1.8.1, you can see through it when it's in your hand, but once placed, it becomes black. My re-textured bedrock blocks go from clear with squiggles in my inventory and hand, to black with squiggles when placed. The same with clear-textured redstone blocks.

Default glass seems to be fine somehow.