A Greek interlinear resource has been made available that seems like it would be helpful. I have not looked at it closely yet, however. Let me know if you have any comments on it.
Go here, log in, and then you should be able to access the downloads directly via the links below:
Another Greek to English Interlinear for eSword that uses Stephanus 1550 with Strong’s numbers and morphology is here.
I also recently created a Textus Receptus Greek to KJV interlinear with morphology resource that is viewable in Microsoft Excel. Please contact me if you would like it and I will get you the link.
Microsoft OneNote (part of the Microsoft Office suite)
Scan and organize your notes to remove the clutter of all those papers.
Automatic text recognition (and searching) for typed information.
Allows you to insert audio in a document, and if you take notes on that audio, it remembers where in the audio your note was taken so you can go back and listen to that particular location again.
Notes can be synced online (for free) and edited there as well.
There is an iPod/iPhone app for OneNote, but note that the free version allows up to 500 notes and then you can’t add any more notes.
You can click and drag whole outline structure sub-trees from one place to another.
EverNote is a popular mobile App.
It’s a quick way to take notes and organize them, with search capabilities.
Recent changes make you get an account, and I think you may have to have online access to use the free version.
The Word and E-Sword allow you to create notes that are tied to Bible passages. You can even create your own commentaries. See the Bible Programs section for more details.
Auto-Insert Verses into MS Word
E-Sword has macros for Microsoft Word that enable auto-insertion of Bible texts. Select the reference, press the button, and there you have it. Pretty neat!
I prefer the other options, but the What the Bible Teaches New Testament commentary series (digital format) is available only here (to my knowledge) for a $20 purchase.
News from the developers: They hope to have the John Ritchie New and Old Testament What the Bible Teaches series included on the standard DVD by around October 2013.
Not for the faint of mind, this is perhaps the ultimate Bible study resource, but comes with a price tag and a learning curve. It features companion apps as well.