Not all pdfs are created equal, so I'll put an asterisk (*) next to those that work well on the kindle due to their size or layout.
SBL Greek New Testament (Kindle) (Everything Else)
The SBL GNT is current eclectic text with an interested TC apparatus. It compares its reading with that of Wescott/Hort, NIV, RP (Byzantine), and Tregelles. If you want to know what the UBS4/NA27 reads just check the apparatus for NIV. When they UBS/NA disagrees with the NIV, SBLGNT will make a note referencing "NA."
UBS/NA, WH, Byz., etc.
This is tagged and parsed. Very nice.
German Bible Society
Has the BHS (Hebrew), UBS/NA, and the LXX (Ralfs) all online.
GNT, LXX, Apocrypha, and Early Church Writings (tagged and parsed)
It isn't the prettiest site in the world, but it sure has a lot of available resources. I have no idea which editions of the texts he's using, but the fact that he's tagged and parsed everything will make me overlook just about anything.
Basics of Biblical Greek Summary (Mounce)*
I've bookmarked all of the pages that have paradigms so I can quickly jump to the appropriate section and check my parsing. Mounce has provided us with a nice summary of his much-adored first-year grammar, but he left out participles... I mean, yeah, who would ever want a summary of everything they need to know about Greek participles?!
"Poor Man's Porter" - A summary of Stan Porter's Verbal Aspect of the Greek in the New Testament
NT scholar Rod Decker wrote this summary for his students. His site is well worth visiting.
Smyth's Greek Grammar for Colleges (Official 1920 edition)
Yes, official is in italics, because the book has paragraph markings, and this is the edition all of the other books will reference. You can find an OCR'd 1916 edition on archive.org, but the paragraph marks will be wrong.
*Update* I have recently read that 1920 is not the official version. Apparently there is a later version from the '50's that classifies as "official."
Grammar of the Greek New Testament in Light of Historical Research (A. T. Robertson)*
This is the third edition with altered pagination. Check out my previous post for a look at the editions.
Syntax of Moods and Tenses in New Testament Greek (Ernest De Witt Burton)*
I got the file from this site, but he didn't embed the Greek fonts into the pdf, so I did it for him.
A Grammar of Septuagint Greek (Conybeare) (PDF)* (Web Only)
I've read that this is more helpful for those who know Attic Greek, as that is what he compares LXX Greek to, but I figure a source has to be better than no source.
The many faces of λυω*
It's everyone's favorite verb in all of it's different conjugations. I have a hard copy of this folded up into my kindle case so I can review it when I'm translating.
Mounce's 8 Rules for Parsing a Verb
Funk's rules for Parsing a Verb
Word Pictures of the New Testament by A. T. Robertson (Kindle File) (Web Only) (PDFs)
Note: only the Web Only link has the entire New Testament. The Kindle file and the pdfs cover 15 books of the NT.
The Expositor's Greek Testament (5 Vols)
Misselbrook's Greek NT Commentary
This site is a treasure-trove of information. Misselbrook is a Greek prof who has developed a 5yr plan to read through the entire GNT. In conjunction with that, he's written textual notes over each day's reading to help you get the most out of it. He has summarized many good commentaries and pointed out where the insight can be found in the grammar of the GNT. This is worth downloading.
Dr. Constable's Bible Study Notes (approx. 7k pages)
While not Greek-specific, and a little less technical, this is akin to Misselbrook's work, but it is over all 66 books of the Bible. He's a seminary prof who has made exegetical and expository notes for each book. The quality seems pretty high, although I haven't perused even a small sampling of the over 7,000 pages available.
Wieland Willker's Textual Commentary on the Greek Gospels (approx. 2,600 pages)
Different than our previous commentaries, this is a Textual Criticism commentary that "discusses the 1500 most important textual variants of the Gospels, plus about 500 minor ones..." This is incredible. The commentary is available in 4 pdfs.
Greek Syntax Notes by Lee Irons
This is like a poor-man's Max and Mary. Irons has gone through the entire GNT and marked out those syntactical elements that are likely to cause the beginner problems and explain them. Very handy.
Liddel-Scott-Jones 8th Edition
This is not the Great-Scott! edition (the 9th), but it is close. The pdf is almost 200mb, so this is best used on your computer.
Liddel-Scott-Jones 9th Edition (Web Only)
You can search this with Perseus. This is the best, most complete, classical-Koine Greek lexicon available. (Of course NT scholars would want BDAG instead, but if you are looking at any Classical Greek at all, this is the lexicon to have).
If you know of other important Greek resources, please let me know!
Other Greek NT Resources
Constance Campbell's Blogged Intro to Verbal Aspect Parts 1, 2, 3, 4, 5
Benjamin Baxter writes a very helpful two-part series on Word Studies in the McMaster Journal of Theology and Ministry: "The Meanings of Biblical Words," and "Hebrew and Greek Word-Study Fallacies"
Craig Noll writes "Biblical Meditation: A Forgotten Resource in Learning New Testament Greek?" His articles makes the case that it is beneficial both spiritually and pedagogically to memorize passages of the GNT.