I know of no verse in scripture that would directly encourage or discourage marking our Bibles. In Bible times, the scriptures were very rare and only in the possession of the few. The scriptures they had were most often written on animal skins and kept in scroll form. There was just nothing in those times to compare to our inexpensive paper copies of scripture.
However, I think we can make some logical conclusions. The only reason for not marking scripture that I can think of (other than having an expensive copy someone wants to preserve) is because we think the holiness of the words of God are transferred to the physical copy and that marking the Bible is a form of desecration. Now, I do believe that a high view of the Holy Bible will result in a certain respect for a copy of the Word. Children need to be taught to treat the Bible with respect. However, the copy of scripture is not holy in and of itself. The physical book is not holy; the words are. The physical book is special because it houses the holy words but it does not have merit in the physical form. There is an important balance here.
But what about marking the Bible? Is it desecration? I do not think so. If I read a chapter in the Bible and one verse or statement means something special to me, then it is natural that I would want that to be remembered. The New Testament authors clearly had special verses in the Old Testament that they used because most verses never got quoted in the New Testament but some got quoted several times. If the marking is done as a study tool, it would be obedience to the scriptures that exhort us to study the Bible. In Psalm 119:31, the psalmist said, "I have stuck unto thy testimonies." I like that. Perhaps he had certain verses that stuck to his heart in a special way. We are to hide the word in our heart (Psalm 119:11), read in the book of God distinctly (Nehemiah 8:8), make the word the joy and rejoicing of our heart (Jeremiah 15:16), and study to show ourselves approved unto God (2Timothy 2:15). If marking important verses helps us fulfill these commands, then there is certainly nothing wrong with us doing it.