As sefiras hamoer reaches its culmination, we are actually concluding two different counts; Chazal (Menachos 66a) teach us that there are two parts to this mitzvah, i.e. the counting of days and the counting of weeks. These two dimensions of sefiras hamoer conclude with the yom tov of Shavuos, which celebrates the completion of both days and weeks. Although we are all familiar with the one-day celebration of Shavuos (with a second day outside of Eretz Yisroel), during the time of the Beis Hamikdash there was an entire week of celebration. Specifically, if a person couldn't bring the korbanos of Shavuos on the first day, there was a week of tashlumin to make up these korbanos.
The Ohar Sameach suggests that there may be halachik ramifications that emanate from the duel count. The counting of days which culminates in the one day celebration of Shavuos does not depend on the Beis Hamikdash as this one day celebration occurs in all places at all times. Therefore, the counting of days is a mitzvah d'oraysa even today. The counting of weeks, on the other hand, which concludes with the week-long celebration in the Beis Hamikdash does not apply midioraysa today in the absence of Beis Hamikdash. This is the rationale for the view of Rabbeinu Yeruchum who maintains that, in fact, the counting of days today is midioraysa, whereas the counting of weeks is midirabanan as a zecher lamikdash.
These dual aspects of counting go beyond the actual mitzvah of sefiras hamoer and subsequent celebration on yom tov; there is a fundamental distinction between the unit of time of a day and that of a week. Days correspond to the physical reality of the earth rotating on its axis. Other units of time, such as a month and a year are also rooted in the world of astronomy - a month measures a lunar cycle and a year measures the earth's revolving around the sun. A week, however, corresponds to nothing in the physical universe. The unit of a week only has meaning because Hashem created the world in six days and sanctified the seventh. The counting of days relates to this world, whereas the counting of weeks belongs to the world of kedusha. Counting of days can exist even without a Beis Hamikdas, whereas the counting of weeks is in the realm of the Beis Hamikdas. Shavuos is the culmination of both counts, because the essence of zman mattan Torahseinu is our ability to count both days and weeks.
Chazal relate to us how the angels tried to dissuade Hashem from giving the Torah to the Jewish People. It was only the response of Moshe that we, as human beings, need the mitzvos of the Torah which are not relevant for pure, spiritual beings such as angels, which ended the argument in favor of giving us the Torah. On Shavuos we celebrate our ability to infuse kedusha into a physical world, our ability to combine the counting of weeks to complement our counting of days.
As we approach the yom tov of Shavuos, we realize that our ability to truly transform our physical world into a world of kedusha is inhibited by our lack of a Beis Hamikdash. Chazal understood that even without an actual Beis Hamikdash we must continue to count weeks, albeit as a zecher lamikdash. It is our constant yearning to once again have a Beis Hamikdash that keeps us focused on the fact that our physical world is not yet complete. As we anticipate the counting of weeks and the celebrating of the entire week of Shavuos in the Beis Hamikdash, we look forward to the day when kedusha will infuse our physical world. When Hashem returns to us that opportunity, zman mattan Torahseinu will have finally achieved its goal. May we merit that day very soon.