Based on this list plus some hunting around on Goodreads for the omnibus editions, I pulled 199 Goodreads ratings for various Warhammer Fantasy fiction releases and re-ranked them by the square of the rating (expressed as a percentage) times the log of the number of raters. The results require finer distinctions than usual to describe them, because of the omnibus editions and the way that series ratings are inflated the deeper you go into the series.
Out of the top 55 titles, these are the most popular Warhammer Fantasy series with omnibus editions, ranked most to least popular:
3. C. L. Werner, Brunner the Bounty Hunter.
4. Nathan Long, Blackhearts.
5. Gav Thorpe, The Sundering.
6. C. L. Werner, Matthias Thulmann: Witch Hunter.
7. Graham McNeill, The Legend of Sigmar.
8. Jack Yeovil, The Vampire Genevieve.
9. Steven Savile, Vampire Wars.
10. Nick Kyme (et al.), Dwarfs.
And here are the standalone novels and series firsts with no omnibuses that managed to rank among those having omnibus editions in popularity:
2. Nathan Long, Bloodborn, Bloodforged, and Bloodsworn from the as-yet uncollected Ulrika the Vampire trilogy.
3. Sarah Cawkwell, Valkia the Bloody, a standalone from the Warhammer Heroes line.
4. C. L. Werner, Dead Winter from the ongoing Black Plague trilogy.
5. Josh Reynolds, Neferata from the Blood of Nagash series.
6. Ben Counter, Van Horstmann, a standalone from the Warhammer Heroes line.
The book by Sarah Cawkwell may be notable not only for being well-ranked but also for apparently being the only title out of 199 that was written by a woman.