Hirhur of Torah
The gemara in Berakhot cites a debate surrounding the halakha of "hirhur." Can someone merely "think" or internally articulate Shema, or must he actually verbalize the words? The mishna in Berakhot (21b) suggests that a ba'al keri (someone who is impure and cannot recite Torah) merely think the words of kriyat Shema since he may not actually recite it. The gemara cites two opinions regarding the purpose of this suggestion. According to Ravina, "hirhur" is "ke-dibbur" (equivalent to speech), and he has fulfilled kriyat Shema through merely thinking the words. Since a ba'al keri is forbidden to actually recite Torah words, the hirhur option is employed. Rav Chisda claims that "hirhur lav ke'dibbur dami." Merely thinking kriyat Shema is insufficient; it must be verbalized in spoken words. The mishna which suggested that a ba'al keri think the words of kriyat Shema then, was merely describing a method for a ba'al keri to not completely deviate from the congregation, which is actively reciting kriyat Shema. He cannot actually fulfill his obligation of Shema through hirhur, but he should still "think" the Shema so that he can join the congregation in "kabbalat malkhut shamayim" (acceptance of God's Kingship).
Since the gemara makes an effort to defend Rav Chisda, evidently we accept his position that hirhur is not akin to dibbur. In addition, the Rabbenu Yona cites a gemara in Shabbat (150a) which also suggests that we rule "hirhur lav ke'dibbur." The gemara prohibits discussion of weekday events on Shabbat (such as asking someone to hire workers for after Shabbat) based upon the verse in Yeshaya 58:13, "Mimtzo cheftzekha ve-dabber davar" (Nor look to your affairs, nor speak about them [on Shabbat]). Since the pasuk specifies "dabber davar" (speaking words), only speaking about these activities is forbidden, not thinking about them. Subsequently, the gemara cites a prohibition for a person to even think about Torah while in the bathroom. Ultimately, the gemara attributes this prohibition to the verse "Ve-haya machanekha kadosh" (your camp all be holy [Devarim 23;15]), suggesting that holiness requires that we not even think about Torah in an impure area. As the gemara isolates this prohibition as an exception based upon a special pasuk, it would seem that in general, hirhur is not equal to dibbur. Based upon these two gemarot (Berakhot  and Shabbat ), most Rishonim claim that we rule that hirhur is not equal to dibbur.
Based upon this ruling, the Shulchan Arukh (OC 47:4) rules that birkhot ha-Torah are not recited over hirhur of Torah. If a person awakes before davening to learn, he must recite birkhot ha-Torah (based upon Berakhot 11b). If, however, he doesn't recite Torah but merely thinks Torah, he is not obligated to recite birkhot ha-Torah. The Vilna Gaon argues with this ruling and claims that unlike other areas of halakha, hirhur of the Torah is, in fact, meaningful and would require birkhot ha-Torah (see the Bi'ur Ha-gra to Shulchan Arukh). Though there are no explicit gemarot which define hirhur of Torah as a mitzva, the Gaon bases his position on both inherent logic as well as the language by which Torah study is described. Logically, it seems unlikely that thinking Torah should not be included in the mitzva of studying Torah. In addition, several verses (such as Yehoshua 1:18 and Tehillim 1:2) refer to Torah study with the term "higayon" – contemplation or meditation in Torah – suggesting that thought is just as much part of the mitzva as actual recitation. How might we defend the position of the Shulchan Arukh, which doesn't require a berakha upon hirhur of Torah?
Conceivably, the Shulchan Arukh might have agreed with the Vilna Gaon about the nature of hirhur of Torah. Namely he might have agreed that thinking Torah is an exception to the general rule that hirhur is meaningless; Hirhur of the Torah is included within the study of Torah. After all, the gemara in Shabbat prohibited thinking Torah in an unclean location!! However, not all Torah requires the recition of a berakha. Even though hirhur is considered a fulfillment of the mitzva to learn Torah, berakhot might only be obligated upon discernable and explicit acts of studying Torah. The laws of berakhot might demand that a berakha only be recited upon a physical and demonstrative act of a mitzva. An analog might be the situation of sitting in a sukka. Theoretically, anyone who enters a Sukka – even without eating - fulfills the mitzva of sitting in a Sukka. Even so, only someone who eats substantive food recites a berakha. Though the mitzva applies "universally," a berakha was only obligated in a situation of an explicit, palpable act of eating.
The same section in Shulchan Arukh rules that birkhot ha-Torah are recited upon writing Torah. In fact, the Taz (a seventeenth century commentary to the Shulchan Arukh) questions the difference between writing Torah (which requires a berakha even according to the Shulchan Arukh) and hirhur (which does not require a berakha). Possibly the answer is based upon the aforementioned explanation. Though any contemplation of Torah is considered a mitzva, only explicit acts of Torah require a berakha. Writing is an official act of Torah, while thinking – though considered a mitzva – is not an outward and discernable performance of the mitzva. In fact, the Ran in Avoda Zara (43b) infers a remarkable halakha about birkhot ha-Torah. He claims that birkhot ha-Torah are not necessary in order to issue a halakhic ruling. If someone is asked to issue a pesak before davening he does not recite a birkhot ha-Torah assuming he doesn't provide the rationale behind the pesak. In this case as well, he is engaging in Torah study (by reasoning to himself the basis for his pesak). However, since he doesn't execute a demonstrative act of Torah study, a berakha is not obligated. The only act he is directly involved in is dispensing halakhic guidance. Even though this act is premised upon reasoning through Torah knowledge, as the act itself doesn't resemble Torah study, it does not require a berakha.
An additional context in which status of hirhur of Torah arises is Tisha Be-av. On Tisha Be-av it is forbidden to study Torah, apparently because this experience generates happiness (see Tehillim 19;9), which is forbidden on this day (see Taanit 30). The Shulchan Arukh (OC 554:3) cites the opinion of the Agur that one cannot even engage in hirhur of Torah on Tisha Be-av. This halakha would further support the aforementioned suggestion that with regard to Torah, hirhur is in fact equivalent to dibbur and considered a fulfillment of talmud Torah. The only machloket between the Shulchan Arukh and the Vilna Gaon, then, surrounds whether a berakha is mandated for purely mental involvement in Torah.
Theoretically, even if we rejected hirhur as a legitimate form of talmud Torah, we could still prohibit it on Tisha Be-av. As the Magen Avraham (554:5) comments, it is not Torah per se which is forbidden on Tisha Be-av, but the joy which Torah produces. In fact, Torah which produces sadness and mourning (reading, for instance, the despairing sections of Eicha or Iyov) is permissible. Even if hirhur of Torah is not actually considered a mitzva of talmud Torah, as it inevitably produces the joy associated with Torah, it should be forbidden on Tisha Be-av. In fact, in light of the Magen Avraham's comments, one has to wonder why this position is not unanimously accepted. If Torah joy is forbidden, then it seems obvious and indisputable that hirhur of Torah should be forbidden on Tisha Be-av. See methodology shiur #37 Aveilut on Tisha Be-av (5755) for a possible solution to this question.