For those who have taken intermediate and advanced coursework in biblical Greek, what did your teachers do for additional vocabulary?
Not much for NT in my minor. But at the University of MN (where I got a major in classical Greek) it was read, read, read, and make a running vocab list of the passage. There were none of the niceties of click-and-parse or click-and-gloss. Each class we had to read two full pages of the Greek text for each class - three times a week. And that was texts which we did not know and had never or seldom read in English.
You need to get a handle on Greek word formation and learn word groups. Metzger's "Lexical Aids for Students of New Testament Greek" is an old one. There are several new books on this such as Trenchard's "Complete Vocabulary Guide to the Greek New Testament." Another older book is "Greek Word-Building" by Matthias Stehle (SBL Sources for Biblical Study 10 Revised by Herbert Zimmermann and Translated by F Forrester Curch and John S. Hanson, 1976).
Being able to identify word roots and split apart words, e.g. ὁδοιπορούντων (Ac 10.9) > ὁδοῖ (ὁδός) + πορεύομαι = travel, be on the way, is an important skill that will increase your vocab quickly.
Identifying English cognates also helps, e.g. ἕρπω, ἕπετον > s-erpw, serpet- , similar to our word serpent and the word herpatology.
I would steer away from more flash cards after you've got the basic 300 words. The problem is that flash cards give you glosses out of context and almost always in the nominative forms. If you want to keep using flashcards, you should start glossing phrases, e.g. προσευχόμενος ἐν τῷ οἴκῳ, ὁδοιπορούντων ἐκείνων (Ac 10.9)
I think you might get more range of vocab by reading through the entire entry of a word when you are stumped. The Middle LSJ lexicon which you can find on Perseus is a great tool for the intermediate student. Go to http://www.perseus.tufts.edu/hopper/morph?
and drag that link to your browser's toolbar. Middle LSJ generally omits all the dialect forms of various words and has mostly gloss information and citations. Also, Danker has an intermediate lexicon (a condensed) BDAG that is useful. The lexicon in the back of the USB (Newman-Barclay) is way too slim to help you and may steer you incorrectly sometimes because it does not have the range of word use that you need to see.