In this week's Parsha, Hashem commands the Jewish people: "לך שבע שבתות שנים וספרת," indicating that they must count seven seven-year cycles in order to culminate with the Yovel in the fiftieth year (ח'ויקרא כ"ה:). The language used in the Posuk is "וספרת לך," "and you (in the singular form) shall count." Chazal learn from this singular phraseology that one counting, namely the counting of the one representative of the Jewish people, the Beis Din, suffices. Sefiras HaOmer, though, is different. The Posuk, in Parshas Emor, uses a different language in connection with this Mitzvah, namely, "וספרתם לכם," "and you all (in plural form) shall count" (שם כ"ג:ט"ו); and the Sifra (שם), as well as the Gemara in Menachos (דף ס"ה:), states that each individual must count the Sefirah for himself, and the Rambam in his Sefer HaMitzvos (מצות עשה קס"א) and the Shulchan Aruch (אורח חיים סימן תפ"ט סעיף א'), rule accordingly.
But how exactly is one to count? The Gemara in Menachos (דף ס"ו.) describes a dispute between Abayei and Ameimar on this matter. Abayei holds that it is a Mitzvah to count the days, and it is also a Mitzvah to count the weeks, while Ameimar holds that one should count only the days and not the weeks; and the Gemara ends off the discussion with the words "אמר זכר למקדש הוא," literally meaning, "he says, it is a remembrance for the Mikdash." What exactly does this phrase mean, and what exactly is this dispute all about?
In order to understand this, the following idea must first be understood. When the Mitzvah of Sefiras HaOmer is introduced in Parshas Emor (שם), it is introduced in a very vague way. The Posuk states, "and you shall all count for yourselves seven complete weeks after the day following the [Pesach] holiday when you brought the Korban Omer as a wave offering, until the day after the seventh week, when there will be a total of 50 days, and you will bring a new grain as a meal offering to Hashem" (שם ובפסוק ט"ז שם). Logically, there are two ways of understanding these Pesukim: either that the Sefirah is dependent upon the Korban, for its only purpose is to count from the time the first Korban is brought in order to know when the second Korban should be brought 50 days later, or that there are two totally independent Mitzvos. The obvious difference would be that if the first view is correct, then today, without a Beis HaMikdash, we would not be obligated to count Sefirah (on a DeOraisa level), while if the latter view is correct, today the Mitzvah of Sefiras HaOmer could still exist on a Torah level.
Based on this, the Rambam in his Sefer HaMitzvos (שם) and in his Mishneh Torah (ומוספין סוף פרק ז' הל' תמידין), as well as others cited by the Mishnah Berurah in his Biur Halacha (או"ח סימן תפ"ט בד"ה לספור), writes that Abayei accepts the second view (that they are two separate Mitzvos), and therefore, there still exists an obligation MideOraisa today, which is to count both the days and the weeks. Ameimar, though, holds that Sefirah is completely dependent on the Korbanos (the first view), and today, consequently, counting Sefirah is only a Zeicher which is MideRabbanan, that is, a remembrance on a Rabbinic level, and therefore the full act of counting both the days and weeks is not necessary, and doing just one of those will suffice. The Chida points out that the word "אמר" used in the statement "אמר זכר למקדש הוא," indicating that it is only a remembrance, is an explanation of the view of the last speaker mentioned, namely Ameimar, which would seem to support the above analysis.
Rashi in Menachos, though (שם בד"ה אמימר), seems to imply that the entire dispute revolves around the statement about "זכר למקדש," meaning that both Abayei and Ameimar hold that Sefirah today is only MideRabbanan (a Zeicher). This is the opinion of most Poskim, such as the Shulchan Aruch (שם) and the Tur (שם); the Ran in Pesachim (דף כ"ח. בדפי הרי"ף בד"ה ומיחייבין) asserts that most authorities hold this way. In fact, Tosafos in Menachos (שם בד"ה זכר) proves this from the fact that during what is called "ספק חשכה," twilight, a time of day when there is a doubt if it is really night yet or not, if one counts the Omer, the Halacha is that he has fulfilled his obligation, because "ספק דרבנן לקולא," meaning that any doubt concerning a Rabbinic matter may be treated leniently, and the person therefore in considered to have fulfilled his obligation.
If this is so, then what exactly is the dispute all about? Why does one authority say that a Zeicher requires counting both the days and the weeks, while the other holds that a Zeicher implies counting just the days? Rav Yitzchak Zev Soloveitchik (חדושי הגרי"ז למנחות שם) points out that our counting is a "מצוה מיוחדת שחכמים תקנו זכר למקדש," "a special Mitzvah which the Chachomim set up to be a remembrance of the Mikdash," which therefore does not necessarily have to follow the rules of the original Mitzvah. For example, during the times of the Beis HaMikdash, outside of Yerushalayim, the Jewish people would take the Lulav and Esrog only on the first day of Yom Tov, and only inside Yerushalayim did they carry the Lulav and Esrog around all seven days of Sukkos. But when the Chachomim set up our common practice, it was as a Zeicher but yet with different laws, for we, even outside Yerushalayim, carry around the Lulav and Esrog even on the last six days of the Yom Tov. Therefore, Rav Yosef Dov Soloveitchik once suggested that the dispute is over precisely what kind of Zeicher Sefiras HaOmer is. Abayei holds that it is a "זכר לספירת העומר," a remembrance of the counting of the Omer which was abolished once the Beis HaMikdash was destroyed, and hence, an exact replica of the former act must be repeated to commemorate it. Ameimar holds, however, that it is more of a "זכר לחורבן הבית," meaning that it falls into the large category of acts which are a remembrance of the destruction of the Beis HaMikdash, and hence, its point is to highlight the destruction of the Mikdash. This is done by intentionally leaving out part of the observance, so that every time one does that act, the participant will be reminded that when there was still a Mikdash, this Mitzvah was done completely, and, hopefully, when the Mikdash is rebuilt we will once again count both the weeks and the days.
With this in mind, the question is why Ameimar specifically holds that the proper form of remembrance for the destruction of the Mikdash is the counting of the days; why not count the weeks? The Sefas Emes (לדברים ט"ז:ט') points out that Sefiras HaOmer is mentioned two times in the Torah, and each time, the Torah seems to stress a different item. In the above Pesukim in Parshas Emor (ויקרא שם), the Torah seems to stress the counting of the days for the purpose of linking it to the Korbanos. But later, in Parshas Re'eih, the Pesukim state "שבעה שבעת תספר לך...ועשית חג שבעות," "seven weeks you shall count...and you will make the holiday of Shavuos (דברים ט"ז:ט'-י); which seem to stress the weeks in the context of counting up to the holiday of Shavuos. Therefore, perhaps, counting the days, which is connected to the Korbanos, would be more of a remembrance of the Beis HaMikdash than would be counting the weeks. The weeks have little connection to the Beis HaMikdash, for they are simply counted to know when Shavuos falls out.
From the above discussion, it seems that there may be two separate aspects of the Mitzvah of Sefiras HaOmer: counting the days and counting the weeks. The Rambam, in his Sefer HaMitzvos שם(), though, emphatically holds this is not so, saying that "one should not err and say that there is a Mitzvah to count the days and a Mitzvah to count the weeks, and one should not think that they are two separate Mitzvos, because they are rather just parts of the same Mitzvah. As a proof, he cites the fact that we count by mentioning the days and the weeks together in the same sentence, which implies that they are part of the same Mitzvah. Another proof may be from the fact that we do not make two Berachos on the two Mitzvos, as we do for example, with Tefillin, which consists of two separate Mitzvos and therefore the Shel Yad and the Shel Rosh each get different Berachos.
The Sefas Emes in Menachos שם(), though, based on his above distinction, holds that there are indeed two separate parts to this Mitzvah, and today, counting the weeks from Pesach until Shavuos still applies on a Torah level, for it is unconnected to the destroyed Mikdash, and therefore was never nullified; there is no reason not to still consider it a Mitzvah MideOraisa, for after all, observing Shavuos is still a Mitzvah MideOraisa. But counting the days, which is connected to the Korbanos, would be only MideRabbanan today. Similarly, the Ohr HaChaim לדברים שם() comments that even if the reason for the counting, namely the Korban Omer, has become obsolete, there is still a Mitzvah from the Torah to count the weeks. Perhaps then, we may reinterpret the Gemara. The dispute there is about what is considered a זכר למקדש, a remembrance for the Mikdash: Ameimar holds that only counting the days is, because only the days are connected to the Korbanos and the Mikdash, while Abayei holds that both the days and the weeks are connected to the Beis HaMikdash, and therefore counting both of them is part of the Zeicher.
Rabbeinu Yerucham (וחוה נתיב חמישי ח"ד תולדות אדם), though, holds the opposite view, saying that based on the Posuk in Parshas Emorויקרא שם פסוק ט"ו( ), it appears that the weeks are connected to the Korban, and therefore counting the weeks today would be MideRabbanan, while counting the days would still have a MideOraisa status. It should be noted that this position is questioned by many, including Rashi (שם בד"ה חמשים יום) and others, who accuse Rabbeinu Yerucham of overlooking the next Posuk (שם פסוק ט"ז) which stresses the days (תספרו חמשים יום), and many also cite the aforementioned Posuk in Parsha Re'eih (בדברים שם) which clearly stresses counting the weeks as a means of counting towards Shavuos, which would leave counting the days as related to the Korban. But the Ohr Someiyach, commenting on the Rambam (הל' תמידין ומוספין שם) defends Rabbeinu Yerucham by citing a Gemara in Rosh HaShanah (דף ה.) which states that there is a "תשלומין" period after the holiday of Shavuos, meaning a period of time to bring the Shavuos Korbanos if one was unable to bring them on time. This "make-up" time described by the Gemara (שם) is a week. Therefore, since the week is most closely associated with the Korban, counting the weeks now, without a Beis HaMikdash, is only MideRabbanan, while counting the days which lead up to Shavuos is still MideOraisa, because observing Shavuos is MideOraisa.