How I cross-reference my Bible

Today I listened to an interview with a seasoned pastor who was asked, "How do you catalog the most helpful parts of the many books you read for future reference?" His response was, "I don't." That is fine for him since he has an amazing memory. I, on the other hand, need to write down references for future use. My present system is proving so helpful, that I thought I'd share it with you in hopes that some of you might find it fruitful to replicate. In simple terms, here's what I do:

• I read with a pencil in hand.  That makes it possible to write notes in the margins and underline significant quotes.  I used to make notes and underline with a pen but do so no longer.  Many of the notes I wrote in books 20 years ago I wish were not there.  Therefore, I only use pencil now so that someday I can erase wrong-headed notes or quotes which I've grown to believe are no longer worth underlining.
• I cross-reference my main study Bible.  Personally, I find most biblical cross-references published in a Bible's margins (Thompson's or otherwise) positively unhelpful.  Some are just plain hard to locate or discern between marginal and footnote references.  Others seem to have nothing to do with the text.  Therefore, I use a Bible for my main study purposes which has large margins, allowing me to write in my own cross-references.  Those references become very valuable when teaching/preaching on a text which is greatly illumined by another part of God's Word.  
• I cite salient book quotations in the margins of my study Bible which help illumine a given text.  This has become the primary way in which I am able to recall in the future and use thoughts I found unusually helpful while reading secondary sources.  This practice adds to the value of my study Bible since it is not simply a copy of the Word of God but a depository of wisdom culled from the minds of great Christians from over the centuries.  An example from the Genesis 3 page of my study Bible is included here.