The most obvious one is genuflecting before entering the pew even when there is no tabernacle up front. Another conspicuous one is kneeling for communion in the line (though it must be said that there is nothing intrinsic to the new form that requires communion lines and side tabernacles).
There are also moments in the Mass itself that strike me as clear imports from old to new. Every once in a while, you will see people genuflect in their pew before the recessional hymn, which I've variously theorized is a unconscious reference to the Last Gospel genuflection that doesn't even exist in the new form.
For my own part, I habitually make the sign of the cross following the penitential rite - not that I've really known why I do this. But I've seen others do the same.
So I was intrigued at this explanation at the site of the Brazos Valley Schola Cantorum, drawn from their norms for Mass.
Penitential Rite: “May Almighty God have mercy on us, forgive us our sins, and bring us to everlasting life”. No sign of the cross. This habit came about because in the Tridentine Mass the Indulgentiam prayer, which followed the Penitential Rite, started with the sign of the cross. Back then, many Catholics would cross themselves during the Penitential Rite in anticipation of the Indulgentiam. At Vatican II, the Indulgentiam was removed from the Mass, however, many Catholics still have the habit of improperly crossing themselves during the Penitential Rite – even though the Indulgentiam is gone.
(Is the wording imprecise here? Was it "at Vatican II" or at the promulgation of the new Mass?)
What can we say about these habits? For my own part, I find it terribly tedious when someone demands that they be eliminated to keep with modern forms -- e.g., someone who insist that people stop genuflecting before entering the pew. Such crackdowns on old behavior presume that everything we do at Mass must have some cognitive/rationalist basis.
The truth is that many patterns of behavior and belief are absorbed from deep history, and it is not always necessary except as a curiosity to know precisely why we do these things. "Ritual" implies a certain routine that frees us from constantly have to think through every action. In this sense, it is like riding a bike: we would be worse at it if we constantly thought about every rotation of the peddle.
So I don't really agree that it is "improper" to do these things. They are part of our history and who we are. Thus will I probably continue to cross myself after the Confiteor, and if you tell me there is no good reason to do so, I will gladly agree, and still persist in doing it. Call it a "superstition" if you want but the action alone carries some inarticulate meaning and significance.
In any case, it seems like an opportunity for comments on other habits that carry no "rational" basis that have been variously absorbed from old to new.