A few months ago I was turned on to Pigma micron pens as a great resource for underlining and taking notes in ones Bible. These pens contain archival quality ink that is chemical resistant, fade resistant, bleed free, and ph neutral. One of the advantages of using archival pens such as these is you do not have to worry about your notes and underlining disappearing over time and I particularly like the idea of using pens that have a very minimal amount of bleed through from page to page as I write in my Bible.
I purchased a couple packs of the above off of Amazon and found the 005 tipped pens to suit my tastes best (005 is equivalent to a 0.20 mm line width). The Pigma micron packs I purchased contained pens in the colors black, blue, purple, green, red, and brown.
Prior to learning about Pigma micron pens I had always used pencil when underlining or taking notes in my Bibles. Now that I have used the micron pens for this purpose I will likely never go back to using anything else. These pens are great! The different colors give you some flexibility with how you want to go about writing in your Bible. I personally like alternating between colors as I underline important verses; however, you could do something like a color coding schema based on topics in the Bible or whatever else your heart desires.
I used to be one of those guys who refused to write in my Bibles. Not sure why; however, I just didn't like the idea of messing up the pages with my crooked lines and chicken scratch. My thoughts in this area have certainly evolved and I really enjoy using these pens as a resource to help me study the Bible.
If you are looking for a resource to use to write in your Bible look no further. Do yourself a favor and pick up a pack or two. You will not regret it! If perhaps you are reading this and are one who seldom picks up the Bible I encourage you to commit a portion of your day to the daily reading of God's word and pray that the Lord will give you a deep hunger to feast upon his word and apply it to your life.