I've found that most students have little to no difficulty understanding the difference between parallel and perpendicular lines when only one plane is involved. Either they never touch, or they intersect at a 90 degree angle, or they just plain intersect. This concept is relatively easy to visualize because it is completely 2 dimensional.

Where the difficulty lies, is visualizing these same types of lines when different planes are involved, since it is 3d. To help, I utilize flash cards, or small pieces of paper. Have students draw a series of lines on each flash cards, making sure there is at least a set of parallel lines, perpendicular lines, and intersecting lines on each, and give each line a name. Then move the flashcards in different ways, either stacking them or making parallel planes, and quiz them about the new relationships between the lines.