As for making textures with blue parts see-through, there's a trick to it. Use the "ToEntity" button(shortcut Ctrl+T) while you have the fence or ladder selected and make them either func_wall or func_illusionary, as you desire(illusionary means you can walk through it).

The next part is a bit hard to explain, but I'll do my best. For textures with blue in them, in which you want the texture to be completely opaque(non-see-through), but have the blue areas transparent, you set the "Render Mode" field to "Solid", because in this mode the texture is still affected by light, which means it will be lighter or darker depending on the light amounts in its area. Set the "FX Amount" field to 255, which will make the blue areas transparent. If you set it to any other partial value, the blue areas will appear black and the entire texture will be translucent, or partially see-through. If you were to set it to 0, the texture would be invisible. This is useful for clipping models, because you can make invisible geometry that blocks nades, players, and bullets, but doesn't affect the good looks of the model.

For textures that don't have blue in them, for instance glass textures or water textures that you want to be partially see-through(like the windows in mini_town), use "Texture" in the "Render Mode" field. Then set the texture to something midrange, like 128. 128 means 50% visible. I believe higher numbers mean less visible, but don't quote me on it, I don't remember offhand. You can still use 255 in the "FX Amount" field when using "Texture" for textures like the one you're talking about, but the visible portions of a texture with blue in it will not be affected by light, so they will appear very lighted even in completely dark rooms, which makes a map just look bad. ;)