What is the single most widely practiced minhag among Jews in Israel today? By "widely practiced" I mean practiced by the most people.
In Israel the custom is to duchen (perform the Priestly Blessing) every day. Outside Israel we Duchen only on Yom Tov.
Celebrating Lag Baomer. Lighting bonfires and going to Meron.
Going to Meron is definitely a custom (the whole celebration of Lag BaOmer is a custom), and according to this article, over 500,000 people were expected to make the pilgrimage in 2009.
According to this, as of Iyar 2011 there were 5,837,000 Jews living in Israel, so that's a pretty large percentage.
As for lighting bonfires, I don't have any numbers, but my understanding is that it is done all over Israel.
Eating Sufgoniyot - jelly doughnuts on Chanuka
Not wearing Tefilin on Chol Hamoed.
Although not based in halacha, Jews standing still during the siren on the yemei zikaron is widely practiced.
Ramban (to Yisro 20:8):
Gentiles count days of the week by the days' names themselves, calling each day by its own name, whether after the heavenly bodies, as Christians do, or by whatever other names. Jews count all the days by the name of Shabas: "echad bashabas", "sheni bashabas", because that's part of the command that we were commanded, to remember [Shabas] constantly, daily.
I seem to recall hearing that this opinion is fulfilled even by calling the days "the first day", etc., without mentioning Shabas explicitly.
Just about every Hebrew-speaker in Israel calls the days "the first day" through "the sixth day" and "Shabas".
Going to the Kotel — the Western Wall. (By the way, this is indeed a custom; Rabbi Yitzhak Yosef Shelit"a in Yalkut Yosef Al HaMoadim).
Hands down it would be lighting the Chanuka Menora outdoors.
Maybe going by one's Jewish name?
Observing 1 day Yom Tov for the Shalosh Regalim (Pesach, Shavuot, Sukkot-Shmini Atzeret).
I would say the "Brit Mila" (besides Sufganyot, as said above, which are given freely at universities, schools, central bus stations, malls etc. etc....yummy. I remember that I even got one at work... Bahurei Yeshiva were giving them away for free in our building in the middle of an industrial park).
The Brit Mila is the one Mitsva that every community in Israel, from Orthodoxes to Kibutznikim Hiloniim, practices without much hesitation; in different ways, but still the Mohel is there and the blessing done. Pydyon HaBen, sadly, is not followed as it should.
edit: this is not a min'hag but rather a mitzva, but still that's the one thing touching every layer of the population. Most non-religious people will look at it as a Jewish custom, like doing the kiddush be yom shishi...
Again, I would say Yom Kippur Observance even if it is Yom Ofnayim.