In no particular order:
Mrs. Humphry Ward, Helbeck of Bannisdale. Arguably her best novel, with characters facing believable spiritual and psychological conflicts, plus (for Mrs. Ward) relatively taut plotting. Its vexed attitudes to both Catholicism and anti-Catholicism are intriguing.
W. M. Thackeray, The History of Henry Esmond. And not just because I wrote about it in Book One. You'd have thought enough people would be into an unreliable narrator with characters grumping away in the footnotes...
Emily Lawless, With Essex in Ireland. Besides having sharp things to say about anti-Irish prejudices, albeit within a Unionist context, it's...brace yourselves...actually funny. The novel parodies just about every major trend in both historical fiction and the earlier national tale, and it has a narrator who sends up Edmund Spenser. (I actually proposed an edition of this a few years back, but the reviewers didn't think the book would sell, alas.)
A non-kiddified edition of Johann Wyss, The Swiss Family Robinson. I was hoping to teach it this semester, only to discover that the only translations currently available have all been made suitable for younger readers.
Grace Aguilar, The Vale of Cedars. OK, this is very niche, but it's a nice rebuttal to Ivanhoe, not to mention Aguilar's only "Jewish" novel aimed at a general audience.
Unaltered editions of George MacDonald's religious fiction. Modern reprints of MacDonald have a bad habit of being reworked for contemporary religious tastes, and therefore cannot be used in classrooms (or for scholarly purposes).
Edward Bulwer-Lytton, The Last Days of Pompeii. Despite my ongoing resistance to my father's suggestion that I edit this novel, there still ought to be a scholarly edition, given that it was something of a cult read at the time (and led to statues, among other things). And, despite the bad writing contest, Bulwer-Lytton is a major Victorian novelist--he ought to be easier to find.
Charlotte Yonge, The Daisy Chain. Granted, this novel annoys a lot of people, but it's nevertheless one of Yonge's most significant efforts.