Question: Is it permissible to stand in silence during the siren on Yom Ha-Shoah and on Remembrance Day for fallen soldiers of Tzahal?
Answer: Some say that it is forbidden on account of "Chukot Ha-Goyim" (following the practices of the non-Jews). This is not "Chukot Ha-Goyim." The Tosafot (Avodah Zarah 11a) define "Chukot Ha-Goyim" as an act rooted in idol worship or devoid of meaning and the Maharik (#88) says that it has a taint of heresy. But it is permissible to do something which non-Jews do if it does not have roots in idol worship and is logical, such as doctors wearing white coats or wearing glasses. Standing in silence for the Shoah or for fallen soldiers is therefore not considered "Chukot Ha-Goyim," since it is to honor them. Furthermore, there are no other nations in which the entire nation stands in silence for a tragedy or for fallen soldiers.
Others claim that this act is "Bitul Torah" (taking time away from learning Torah). But there is no problem to think about Torah or learn Torah by heart related to the self-sacrifice during that time.
I once saw in the name of the Kabbalist, Ha-Rav Ashlag, that the siren has an aspect of wiping out the memory of Amalek similar to making noise upon hearing Haman's name. If this is so, then there is certainly no problem. It is difficult to agree or disagree since it is not clearly exact how this wipes out the memory of Amalek.
Regardless, the entire community stands in silence for the Holocaust or for fallen soldiers and one should not separate himself from the community. There are certainly better paths in our traditions for remembering the deceased – learning Mishnayot, reciting "Kel Maleh Rachamim," etc… - but here one should not separate from the community.