In the Siddur of the Alter Rebbe, we find a seeming anomaly with regard to Sefiras HaOmer. Although the text and order of his Siddur is based on that of the AriZal,² the Alter Rebbe concludes his Siddur with Sefiras HaOmer, unlike the other Siddurim of the AriZal that conclude with the festivals of Shemini Atzeres and Simchas Torah.³

We must perforce say that since "All goes according to the conclusion,"⁴ the Alter Rebbe desired to conclude his Siddur with Sefiras HaOmer, inasmuch as it sheds light on and is uniquely related to the entire concept of prayer. But what relationship is there between the two?

Mitzvos are generally divided into two categories: commandments that require specific actions or speech, such as wearing tefillin, relating the tale to the Exodus, etc., and mitzvos that are "duties of the heart," such as love and fear of G-d - commands that are dependent upon the person's intent and feeling.

The mitzvah of prayer is unique⁵ in that, although prayer must be verbalized,⁶ nonetheless the act of prayer requires "that the person supplicate and pray daily,"⁷ i.e., it is a manner of service that is entirely related to the individual's feeling - without this feeling of supplication the person's speech and words of prayer are not considered prayer at all.

Herein lies a striking parallel to Sefiras HaOmer. The Alter Rebbe rules: "It is permissible to count [the Omer] in any language that he understands. However, if he fails to understand the language with which he counted, then, even if he counted in Hebrew... he has not fulfilled his obligation, for since he does not know the count, it is not considered counting at all."⁸

In other words, with regard to Sefiras HaOmer, the commandment lies not in verbalizing the count (although it is indeed necessary to verbalize it),⁹ but rather in the person's knowledge of the actual count, without which "it is not considered counting at all."

There is yet another strong similarity between prayer and Sefiras HaOmer. Prayer places the person on a very holy plane;¹⁰ when a person prays, he is on a much higher spiritual and sanctified level than usual.

This aspect of holiness too is stressed in Sefiras HaOmer, for each night after counting the Omer, we say: "You have commanded us...to count Sefiras HaOmer in order to purify us...and sanctify us with Your supernal holiness."

Prayer also differs from other mitzvos in that most other commandments are fulfilled by doing the deed itself - and in a more comprehensive state, by doing the deed accompanied by its proper intent.

Prayer, however, is very different: On the one hand, prayer involves supplicating G-d that He fulfill the person's request; on the other hand, fulfilling the commandment of prayer is not at all bound up with the person's supplication and request actually being granted - his very supplication entirely fulfills the commandment of prayer.

Here, as well, Sefiras HaOmer bears a striking resemblance to prayer:

According to many of our sages,¹¹ the concept and mitzvah of Sefiras HaOmer serves as a preparation to the festival of Shavuos, the time when G-d gave us the Torah. In the words of the Chinuch: "We were commanded to count from the morrow of the festival of Pesach until the day of the giving of the Torah, in order to demonstrate our great desire to reach that revered day...For counting [the days until a given day] demonstrates that the person's entire yearning and desire is to reach that particular day."

Notwithstanding the fact that Sefiras HaOmer acts as a preparation to Shavuos, it nonetheless is a mitzvah unto itself, with its own individual blessing, etc. - just as prayer involves beseeching G-d to fulfill a request, and nevertheless is considered a completed commandment, even if the person has yet to merit that his request be granted.

Based on Likkutei Sichos, Vol. XXII, pp. 114-119

Footnotes: 

1. Vayikra 23:16:17. 
2. As stated in the faceplate of his Siddur. 
3. See Siddur HaRash m'Rashkov; Siddur HaAriZal Kol Yaakov. 
4. Berachos 12a. 
5. Cf. Beis Elokim of the Mabit, Shaar HaTefillah ch. 3. 
6. See Magen Avraham, Orach Chayim 101:2; Shulchan Aruch Admur HaZakein, ibid., subsec. 4. 
7. Rambam, Hilchos Tefillah 1:2. 
8. Shulchan Aruch Admur HaZakein, 489:10. 
9. Ibid., subsec. 1. 
10. See Likkutei Torah, Chukas 66a. 
11. See Moreh Nevuchim 3:43; Chinuch, Mitzvah 306; Ran, conclusion of tractate Pesachim.