www.biblegateway.com - I look up verses using keywords or verses; excellent reference for almost every version of the Bible in many languages.
http://studylight.org/com/ - Tons of commentaries; I use this site to read commentaries when I am having trouble with understanding something, in addition to talking to my pastor.
www.biblestudytools.com - I use this site mostly to look up words in the Greek and Hebrew (the interlinear Bible), but excellent for creating an online Bible and getting references. There's a place for notes of your own and to look at other, normal people's notes and pastors' notes as well.
E-Sword - a free Bible software download. Only available for PCs right now. I haven't been able to use it since I do not have a PC, but I have heard it is amazing.
The Bible study will come along shortly! Here it is:
I am currently going through the Discipleship Journal in addition to Beth Moore's study on Seeking a Heart like His: A Study on David.
Or pick one of three plans, whichever works for you! http://www.navpress.com/dj/content.aspx?id=138
Here are short Bible studies to enhance your time with the Lord: