John ch. 14:

"Dicit ei Thomas: Domine, nescimus quo vadis: et quomodo possumus viam scire?"

I am wondering why "Him" is not accusative here?

Also, I am having a hard time wrapping my mind around the subjunctive. could someone briefly summarize the subjunctive, well... the usages - perhaps some kind of formulated system you came up with to personally help yourself? or maybe where I can find a very concise explanation of the forms and usages of the subjunctive?

The reason ei is dative is because he is being addressed. Remember that Dative is translated (usually) "to/for..." See also the dictionary entry for dico in L&S: "The person addressed is usually put in dat."

http://perseus.uchicago.edu/cgi-bin/phi ... isandshort

This makes sense because the natural direct object of speaking is the thing spoken (i.e. the words or ideas) and not the person spoken to. "Thomas says to Him..."

Subjunctive is, broadly speaking, contrasted with indicative in that the indicative mood indicates simple fact of how things are, whereas subjunctive is more how things could be (would, could, should, may, might etc.). That is at least the rough principle. Of course, in actual usage, there are specific constructions governing their use. I suggest just reading through a grammar like Allen and Greenough or even one of those compact quick-reference grammars. A&G begins its treatment here, though I would recommend using a physical copy or a PDF scan (Google it) for easier navigation.

http://www.perseus.tufts.edu/hopper/tex ... ythp%3D436

I wouldn't worry about memorizing everything immediately. Focus on some of the more important ones (like present subj. as main very, which is called hortatory or jussive, or ut + subj. verb, which is a purpose or result clause).

The direct object of "dicit" is what Thomas said.