If I don't consider them gaping holes after almost 30 years of collecting the stuff, I guess they aren't gaps for me.
I really cannot think of anything except for opera I'd consider glaring holes in the "standard repertoire". This is partly due to the fact that other somewhat gappy fields are music of the last ca. 70 years and before 1700 or 1600.
But in opera, I have only one by Donizetti, two by Bellini (and I don't think I listened to both), 3 by Rossini, gaps in Verdi and Puccini, no other Verismo, no Gounod, Massenet, only 4 of Strauss's, none of Prokofieff's...
Overall, I'd say my fault is more on the side having stuff on my shelf for "completeness" I (almost) never listened to (e.g. quite a few of the operas I do have). But I also have gaps in stuff I generally like, e.g. some of the lesser known Handel oratorios, no complete Scarlatti sonatas, Bach cantatas or Schubert Lieder... I also lack a recording of the earliest Brucker symphony in f minor... but I have 0-9, including alternative/earlier versions of 3,4,8.