What do you mean by "Waffled"...? Not a term I'm familiar with, sorry Please Register or Log in to view the hidden image!
I think he means he likes to eat waffles while watching star trek. Along similar lines, other people also make note of the enterprise D being cheesey tubed, donuted, pizzaed or popcorned.
i am referring to exterior shots of the ship. in some episodes the ship appears smoothed skinned although there are slightly different colored squares on it. in the "waffled" episodes the ship appears to have square shaped bulges on it, especially the saucer section.
Please Register or Log in to view the hidden image! As the high definition and computer animation has gotten better you'll see the "plating" on the hull better. Those plates represent the way they put the ship together piece by piece, welding plate to plate not just one entire gigantic piece of material.
the image above shows the "smooth" enterprise. the squares seems to be painted on. the appearance of the "waffled" enterprise is different and distinct. i'll be going through my episodes and i can give some episodes where this happens. the explanation of an "improved" enterprise doesn't work. a "waffled" enterprise can be seen between 2 episodes with a "smooth" enterprise.
They used several different sized studio models when shooting Next Generation. ( it actual was one of the last TV series to use actual physical models). the model used in any particular shot depended on the need. It is likely that only the largest or "hero" model had the extra detailing in surface detail. Also, how well you are able to see the "bumpiness" of the surface depends on how the model is lit. In the above shot the lighting come from pretty much straight above, which tends to hide irregularities in the surface. Another factor is the intensity of the illumination. Higher illumination levels also tend to wash out the shadowing that highlights the differences in the surface. This is in part due to the effect of radiosity, where light reflected off of lit surfaces illuminates shadowed ones. Changing the angle and level of the illumination, can have a dramatic effect on how a surface appears. The same surface can go from looking smooth to looking bumpy.
Janus has pretty much covered it - it is stated that several sections of the Enterprise were covered in armored plating to give some measure of protection if/when the shields failed in combat, notable the Stardrive Section near main engineering, the Bridge, and the Impulse Drive Manifolds. However, the type and appearance of the armor is never explained (in the tech manuals and other media it is hinted at possibly being a more... conservative... use of the Ablative Armor that the Defiant and Sovereign classes are clad in, which would make sense as the Ablative Armor IS stated to be horribly difficult and expensive to produce, making it something you wouldn't lather a non-frontline ship with)