Gemara

(Beraisa): One left a barrel of wine, and to tithe his wine he would declare that (the proper amount of) wine in the barrel should be Terumah. Once, he checked the barrel and found that the wine had become vinegar (Terumah of vinegar does not exempt Tevel wine). The first three days are definite; past this is doubtful.

Berachos 21a (Rav Yehudah): If one is unsure whether or not he said Emes v'Yatziv, he must say it.

He holds that Emes v'Yatziv is mid'Oraisa.

Rishonim

Rambam (Hilchos Terumos 5:24): If one had a barrel of wine from which he used to declare Terumah, and he checked the barrel and found that the wine had become vinegar, for three days after he last checked it; the Terumah was Vadai wine. After this, it is Safek, and he must take Terumah again.

Rif and Rosh (Berachos 6a and 1:14): The Gemara did not resolve the law of one who began to bless on wine and finished the Berachah for beer. Therefore, he does not bless again, for we are lenient about a Safek mid'Rabanan.

Tosfos (Berachos 12a DH Lo): The Ri says that we are stringent, and he must bless again.

Rif and Rosh (Berachos 12b and 3:15): If one is unsure whether or not he said Emes v'Yatziv, he must say it, for it is mid'Oraisa.

Rosh: The She'altos learned from here that one need not repeat any Berachah mid'Rabanan if he is unsure whether or not he said it.

Rambam (Hilchos Berachos 4:2): If one is unsure whether or not he blessed ha'Motzi, he does not bless again, for it is not mid'Oraisa.

Poskim

Shulchan Aruch (YD 331:65): If one made a barrel of wine Terumah to exempt wine, and he found that the barrel was vinegar, if he is unsure whether it was wine at the time he made it Terumah, it is Terumah, and he must take Terumah again. The same applies if one separated a melon and it was found to be spoiled.

Shulchan Aruch (OC 209:3): If one has a Safek whether or not he said any Berachah, he does not bless, either before or after. The only exception is Birkas ha'Mazon, for it is mid'Oraisa.

Taz (3): Birkas ha'Mazon is mid'Oraisa if he ate to satiation. Many Rishonim hold that Birkas me'Ein Shalosh is also mid'Oraisa. Therefore, Acharonim say that if one ate to satiation from the seven species and is unsure whether or not he blessed, he should eat another k'Zayis of the same species and bless.

Mishnah Berurah (167:9): Since ha'Motzi is mid'Rabanan, we are lenient about the Safek. Even if he wants to eat more, he may not be stringent to bless, for it is unnecessary. If someone else will make ha'Motzi, it is proper to be Yotzei through his Berachah.

R. Akiva Eiger (Teshuvah 1:25 DH uv'Yoter): Emes v'Yatziv is mid'Oraisa, for one must mention Yetzi'as Mitzrayim. One could mention it without a Berachah. Why may one bless mi'Safek? Rather, even if he really said it already, since Chachamim obligated him to repeat it, it is not an unnecessary Berachah.

Question (Magen Avraham 3): The Ri (in Tosfos above) obligates one who began to bless on wine, and finished the Berachah for beer, to bless again What is the reason? We are lenient about Safek Berachos!

Answer #1 (Magen Avraham): Perhaps Tosfos holds that Mitzvos require intent. Since he intended for something else, he was not Yotzei.

Answer #2 (Pnei Yehoshua Berachos 12a DH Lo and DH v'Yoter): 'We are lenient about Safek Berachos' means that one need not bless again. He may if he wants. Here he must do so, for one may benefit without a Berachah!

Answer #3 (R. Akiva Eiger, based on Maharsha and Rashba, Pesachim 102a): We are lenient about a Safek Berachah when it is not Me'akev, e.g. Birkos ha'Mitzvos. Here, one may not drink without a Berachah. In any case his Berachah was l'Vatalah, so blessing again is not a Berachah l'Vatalah. Normally, if one is unsure whether or not he blessed, he may not bless again, lest he already blessed. The Rif holds that we are lenient about Safek Berachos, and he may eat

Chelkas Yo'av (OC 58): The Rambam holds that one is Yotzei Berachos through thought. The Halachah does not follow him, but if one did not pronounce the words due to sickness or Ones, he was Yotzei (Magen Avraham 185:1). Here he is Ones, for he cannot eat (perhaps the Halachah follows Tosfos), and he cannot bless (perhaps the Halachah follows the Rif)! R. Akiva Eiger (184:4 DH Mionei) cites Ginas Veradim, who says that one should think the words of any Safek Berachah mid'Rabanan, to be Yotzei according to the Rambam.

Rav Pe'alim (3 OC 7 DH u'Mah): Many Acharonim say that when one has a Safek, it suffices to think the words of a Berachah. Some say that the Isur of Shem Shamayim l'Vatalah applies even to thought.

Aruch ha'Shulchan: There is no Isur to say 'Rachmana', even 100 times. If one has a Safek whether or not he must bless, he should say 'Baruch Rachmana ...' I myself do. I totally disagree with those who consider this a Berachah l'Vatalah (e.g. Chasam Sofer Nedarim 2a DH Hineh).

Question (Mishbetzos Zahav OC 219:3): Why do we say 'Baruch Rachmana who gave you...' for a friend who is not so dear? If Rachmana is not a name of Hash-m, we should say 'Baruch Rachmana Malka d'Alma...' (without concern for Berachah l'Vatalah)! The Taz forbids. Also, why are Safek Berachos Lehakel? We should bless in Arame'ic! Perhaps one may not because Malka d'Alma shows that Rachmana refers to Hash-m.

Answer (and rebuttal of Aruch ha'Shulchan - Chavas Da'as YD 110 b'Veis ha'Safek 20): Normally, one repeats a Mitzvah if he is unsure whether he was Yotzei. We do not take the Lulav on the eighth day (in Chutz la'Aretz), for a Safek Mitzvah does not override an Isur (Muktzeh). Otherwise, we repeat a Mitzvah such as Lulav of Sefiras ha'Omer without a Berachah. According to the opinion that Kri'as Shema is mid'Rabanan one does not repeat it due to Safek. One may say Shema voluntarily, but not for a Chiyuv if one is exempt. The Rosh permits praying Nedavos the entire day, but not to pray for a Safek Chiyuv. The same applies to all Berachos. One may bless Nedavah, even with Hash-m's name, just like he may pray Shemoneh Esre Nedavah. One may not bless for a Safek Chiyuv, even without Hash-m's name, for we find that one can be Yotzei without Hash-m's name, e.g. 'Baruch Rachmana Malka d'Alma...' I defend those who say Baruch Atah Hash-m in Maa'mados and requests, since it is not for a Chiyuv. This is like Piyutim and Mizmorim, which bless Hash-m with His name. Likewise, one may answer Amen needlessly, but not an orphaned Amen (long after the Berachah).

Ha'Emek She'elah (53:2 p.340) and Meshiv Davar 2:30:3 DH Mah): One may say 'Rachmana' for naught, but some Gedolim forbid l'Shem a Berachah. Chazal did not suggest this for Safek Berachos. One may say Amen for naught, but not after an invalid Berachah, for this is like Sheker.

Chelkas Yo'av (YD 173 DH Ayen): For every Safek Berachah, one should say 'Baruch Atah Hash-m Melech ha'Olam...', like the Rivash (408) says.