John, I don't know if you got to talk to Chris much but since he was Head of Deck checks, he ran into all kinds of problems with marking of cards.
First, all duelists should familiarize themselves with item 12, paragraph 2 in UDE tournament policy. Where it says "players will not apply decorations [or markings] that obscure a significant portion of the card's image or text", most judges will not tolerate any writing or artwork that obscures any portion of the effect text. If judges can't read the text because you have obscured it, you can't use the card!
Next, don't alter the name or Stats of a card. As a judge the only reasons I can see for a player to alter the name of the card or it's stats is either stupidity or to cause confusion. One player wrote "#2" immediately behind the title of his "Morphing Jar" monster card. Don't ask me why he did this? "Morphing Jar" and "Morphing Jar #2" are 2 different cards. Needless to say, he had to replace the card.
Signed cards were allowed. However, if there were ballpoint pen marks that showed up through the card back that could be felt or seen with sleeves, then the card is considered "marked" and unuseable for tournament play.
Coloring of the artwork or the face of the card is the most difficult to call because there is some subjectivity to it. It is up to the judge. In general, I would avoid any markings altogether.
doc