the Skeptic's Annotated Bible is my favorite. I don't know if it is available in other formats though. It is still a great place to go to drop piles of quotes that violate science, are inconsistent, or are unjust.
I realize I am a little late on this post, but I figured that even if you have already decided on a Bible then at least maybe something I share may be helpful in some way. A couple things:
1) If you are looking to just have a reference resource at your disposal for debating and such, then I would say use a website like www.biblegateway.com or www.blueletterbible.com as these sites offer excellent search functions and have just about any translation that you might need. I prefer biblegateway personally. They would would also be good sites to compare the various translations for any hard or digital copies you may decide to invest in.
2) What you should know about translations and error. You may already know a lot of this, but i will share anyways. The O.T. is written in Hebrew and Chaldee and the N.T. is in Greek. The problem with translations is that when translators make their translations (KJV, NKJV, NIV, NASB, YLT, etc etc) the products lie on a spectrum of interpretation from literal to paraphrased.
The more literal the translation, the more accurate it will be though some people don't like these cause they tend to be harder to read and the "all-knowing" heads of theology seem to think the subtle cultural references and such will be lost on the average reader. Thus there tends to be a stronger push to the other end of the translation spectrum - paraphrase.
The problem with the paraphrase is that these Bibles are translated in a way that leaves the meaning of a text solely in the hands of the translator. They read the test, decided what it means and then put this in english...thus the reader is forced to succumb to the translators own theological bias and agendas consciously or subconsciously.
A quick example it the word "hell". The concept of hell as taught by the western church is not of Jewish origin. It is not in the Jewish scriptures and Jesus taught from the Jewish scriptures, therefor, he did not teach "hell" as an afterlife of eternal torment like the church says he did. So, if we look at translations, the most literal translation that we have "Young's Literal Translation" doesn't contain the word "hell" in it at all while one of the least literal "King James Version" contains it 54 times. (I would love to go into more detail regarding this particular word study if anyone is interested...maybe I'll start a thread on it soon :)
So, the point is, if you want the least amount of bias, I would go with the more literal translation. Young's Literal Translation is the best, they ascribe one english word to the closest Hebrew or greek equivalent and use it in a 1:1 ration no matter how it sounds. The trade off it that the wording can be a little funny sometimes, but anyone who does well in reading and english should be fine.
I would also look at the New American Standard Version if the Young's is a little too tough to read. The NASB is prob about the second most literal and is a much easier read.
A comment or two about other translations:
NIV - Widely popular esp among evangelical christians, but very inaccurate and full of western christianity doctrine. This is a very easy read and is great if you want to develop the same perspective on doctrine and teachings that most of the US has, however, you will most probably miss the truer deeper meanings. And with the truth of the texts in hand, you can take on anyone.
KJV - I love this translation for leisurely reading, it is elegant and flows well, however, the translation is soo inaccurate (as even admitted in the margins in many places by the translators) that I would not ever recommend this for serious study. The only usefulness as a study tool is that it goes hand-in-hand with Strong's Exhaustive Concordance which is a must-have for any seriously studying the bible. Also, it is considered by older more fundamental christians as the only one "true" translation and of course this is IMO, crap.
As far as the study bibles that have been mentioned that also have historical notes would be a great idea. Parallel bibles are cool, but I would pick maybe a study bible that is just one translation to start.
Also, if you want an awesome unbiased source of instruction on the history and accuracy of scripture, check out some of this guy's books: Bart D. Ehrman He is a doctorate professor at Harvard, if I remember correctly, and he set out to learn greek and hebrew so that he could study teh scriptures for himself. He offers such an excellent and unbiased perspective that even seen books written like this one which are written by dogmatic Christians who have had their foundational beliefs rocked by the awesomeness of Ehrman's critical and frank analytical study of the scriptures.
As far as reading the scripture, definitely start in the New Testament and read is in order from Matthew onward. The Old Testament is a little tougher but after the New Testament, I would go back to genesis and just read in order from there. That is what I did and it worked really well for me. I actually used the NASB, for that study and now use that one and the YLT for my study.
After all of that, if you want to go even deeper, I would suggest delving into the Dead Sea Scroll collection and even the Nag Hammadi library. Very interesting to compare those to what we see in the canonized bible and especially when we allow seek Ehrman's tutelage regarding scripture and church history. I am very tempted to suggest that you read some of Ehrman's stuff first so you have a really good idea on the origin and the context of the scripture before you actually read it...I think that might be most beneficial to you, but that is just a suggestion.
So, 1) Understand the history, 2) study the texts in the Bible (literal translation) and use a concordance to reference back to the greek and hebrew 3) Read the extra-biblical scriptures (Dead Sea, Nag Hammadi) and 4) stand tall in your equipping being very confident that you will be ready to take on even the most learned christian apologists and/or anyone for that matter :)
My $0.02 :)