The best version, I feel, is the one you actually read.
I'd like to touch (breifly) on the "NIV cuts things out" thing.... yes, the NIV drops some verses out (most of which are repetitive things that make more sense when you understnad culture at the time)... however all but 1 NIV that I've owned has every one of those verses foot-noted at the bottom of the page (the one that doesn't cost me something like $1-3 at Walmart and is obviously a cheap production).
Actually my advice is learn Greek and Hebrew and read the books in their original text (Hebrew for OT, Greek for NT). But that's not even a complete picture of understanding the scriptures.... as others have said, you'd basically want to attend a Jewish school or something and not only learn Hebrew, but also the historical culture of the Jewish people as well. Go learn some about the other cultures and communities of the day that the books where written (the NT consists of letters that where written from one person to another or a group, so you'd need to understand the situation of each of these people as well).
Obviously this is a lifelong pursuit, and in the end that's what we're left with.. but in the meantime.......
Notes and other writings about different books of the Bible are good for understanding, but don't take any one as dogma, each is writen by a person and may be wrong, you'll find as many opinions of what a verse means as there are writings.
Me, I've been carrying around the same NIV for years, it's a student bible that I was given years ago (actually, it's the leather/imitation leather version of the one I was given years ago). I have a KJV, NKJV, and a few others around here, and I use each one at one time or another (the NKJV is a large print with some extra cross-reference info for example). I also had a copy of the Online Bible for years (haven't been real happy with the windows versions though, since bought one of Logos' collections, but I don't currently have it installed). A Strong's concordance with a Greek/Hebrew lexicon is a big help (again, my favoriate way to use these was the old DOS version of Online Bible, I've also used the one with my Logos software as well as some of the other comptuer bibles I've owned).
I personally can't stand the Amplified Bible, not that it's a bad translation, I'd say use it for study (along with some other resources), but I know too many people who get it, use it for reading out-loud, and read EVERY DARN WORD printed on the page.
Many people like KJV because they feel it's poetic, I personally can't stand "Old English," and find it difficult not only to properly understand (it's too easy to miss-understand things because of words that have changed meaning since that translation was made or because of the subtle things that are a part of that form of English). I'm also a stickler for those who use it because they feel it sounds more "spiritual" than regular modern english. Frankly on that issue if Jesus walked among people today, I'd believe Him saying "Yo, Wazup" much sooner than "How art thou," but that's just me
The Message is good for reading, but difficult for study as it doesn't have verse numbers, and you have to trust that the people who put it together have properly understood what the scriptures where actually saying since it's more paraphrase than literal.
For study I'd say get as many different ones as you can, of the good ones anyway, study them side-by-side along with the Greek/Hebrew cross references (Strongs/Lexicon combo), and pray, pray, pray.
er... welll.. I guess I'm done. Anyone else want to use this soapbox now?