I'm studying Greek exegesis as part of my M.Div, and i've been lamenting my lack of a really good software tool for translation and exegesis.  The way my workflow (following a manual, pen & paper process) generally unfolds as follows:

1. Read through the verse in Greek.
2. Parse the forms of nearly all verbs (excluding some of the most common ones).
3. Check my parsing against the morphology in my Pocket e-Sword or Logos 2.1 software.^[1]
4. Note any vocabulary unfamiliar to me, including parsing the particular form in the text and noting the definition.
   
5. Translate the verse for myself.
6. Note any questions, comments on translation, or points of debate from an exegetical perspective.
7. Check the textual variants in the NA²⁷ and/or UBS⁴.  If any of them present themselves as likely alternatives to the text, repeat steps 1-6 for the changed text.
   
8. Check my translation against a more literal English translation such as ESV, NASB, or RSV.
9. When i've reached the end of the pericope or chapter, read through some commentaries and revise my translation, textual choices, and notes in the light of my reading.
   

This is a fairly laborious process that could use some software assistance.  Here are the parts of the process i think could benefit most:

1. Entering and checking parsing of each word (by providing a simple entry field for each word, colouration to indicate correctness, and a one-click interface for revealing the correct parsing).  Parsing tags should be customisable in order and encoding process so that i can choose one that is familiar to me.
2. Noting any vocabulary likely to be unfamiliar (based on word count frequency, or better yet, my previous record in vocabulary retention).  The software should provide a very simple way methods to:
• show/hide the root form of a vocabulary word.
  
• check whether i remember my vocabulary correctly (by hiding the meaning by default and having a reveal button)
• allow fine-tuning of which words are marked as vocabulary words (by providing a button to mark a word as already known, and allowing me to right-click words in the text to manually add them to the vocabulary list)
3. Choosing possible English renderings of a given word or phrase.  Obviously one of the ways of doing this is checking against the English translations, but doing this too early in the translation process is "cheating", IMHO.   One of the most useful tools i've found in this respect is the key to the BAGD lexicon, which gives you the root form of the word, tells you which page & sector (A, B, C, or D, corresponding to top left, bottom left, top right, and bottom right, respectively) it's on in the lexicon, and the suggested English meaning.  A similar technique in Logos 2.1 is to do a reference search through BAGD on the verse in question.^[2]
4. Recording verse notes with my translation that will scroll appropriately, and appear on any printouts.
5. I've not used any software that handles textual variants well at all.  Pocket e-Sword (GNT-V module) just displays them in the text with superscript letters indicating which textual tradition they're found in.  This makes it hard to read the text.
6. Checking against other English translations should be fairly easy to achieve in most Bible software, but it needs to be easy to pick & choose which translations on a verse-by-verse basis, and not require adjusting a global preference.
7. Performing a reference search for the verse under consideration in all language-related tools and commentaries so that important points can be covered in the notes.  Logos 2.1 does this pretty well, but many of the useful works available in that form are not available for Free Software Bible applications.

Some other thoughts that would tie in well with this process:

1. Being able to tag vocabulary words and then print lists or cards for later reference.  An option for printing the word frequency in the Bible and the places i've tagged it as vocabulary should be included.
2. I don't own a laptop, so i don't usually have a computer (other than my Dell X50v PDA) with me in class, thus good printing support (including export to PDF and HTML) is important.  Having options to show/hide original text, textual variants, verb parsing, roots & definitions, and translation (both mine and others) should be included.
3. It would be really nice to have a way to show/hide accents (and possibly breathings) in Greek texts, since they're not used most of the time.
   

All of this seems a big ask, but it surprises me that i've never seen it before.  I own copies of a fair cross-section of Bible software for Windows (although not BibleWorks).  I suspect there are also a lot of similarities to the process followed by the translation team on the NET Bible - what did they use?

I'd appreciate any feedback on the process and features i've described above.

[1] Yes, i know Logos 2.1 is very old (built for Windows 95), but it's a much easier and faster tool to use than its successor, Libronix DLS.  Describing the performance of the passage study tool in Libronix DLS would require me to use some rather un-Christian words. 
[2] Another assistance in this step is the Libronix DLS word frequency graph (count in each book of the Bible).