These are the recognized health benefits of natural (non-alkalized or non-Dutched) chocolates, together with examples of scientific references (not comprehensive, there is a huge number of studies published). Almost all the studies quoted can be found on PubMed, the official US medical reference database:
In the American diet, fruits, vegetables, tea, wine and chocolate are major sources of antioxidants, which have been shown to have protective effects against CVD
Fraga CG, Actis-Goretta L, Ottaviani JI, Carrasquedo F, Lotito SB, Lazarus S, Schmitz HH, Keen CL: Regular consumption of a flavanol-rich chocolate can improve oxidant stress in young soccer players. Clin Dev Immunol 2005, 12(1):11-17.
Kris-Etherton PM, Keen CL: Evidence that the antioxidant flavonoids in tea and cocoa are beneficial for cardiovascular health. Curr Opin Lipidol 2002, 13(1):41-49.
Steinberg FM, Bearden MM, Keen CL: Cocoa and chocolate flavonoids: implications for cardiovascular health. J Am Diet Assoc 2003, 103(2):215-223.
Chocolate flavonoids have shown good dose-response bioavailability in humans. There exists several mechanisms of how flavonoids may be protective against cardio-vascular disease. These include: antioxidant, anti-platelet, anti-inflammatory effects, as well as possibly increasing HDL, lowering blood pressure, and improving endothelial function.
Richelle M, Tavazzi I, Enslen M, Offord EA: Plasma kinetics in man of epicatechin from black chocolate. Eur J Clin Nutr 1999, 53(1):22-26.
Wang JF, Schramm DD, Holt RR, Ensunsa JL, Fraga CG, Schmitz HH, Keen CL: A dose-response effect from chocolate consumption on plasma epicatechin and oxidative damage. J Nutr 2000, 130(8S Suppl):2115S-9S. [PubMed Abstract]
Heiss, C. . . . H. Schroeter, et al. 2005. Acute consumption of flavanol-rich cocoa and the reversal of endothelial dysfunction in smokers. Journal of the American College of Cardiology 46(Oct. 4):1276-1283.
Schroeter, H. . . . C. Heiss . . . C.L. Keen, N.K. Hollenberg, . . . H.H. Schmitz, et al. 2006. (–)-Epicatechin mediates beneficial effects of flavanol-rich cocoa on vascular function in humans. Proceedings of the National Academy of Sciences 103(Jan. 24):1024-1029.
Chocolate has been shown to be protective against heart attacks.
Nutrition & Metabolism 2006, 3:2 doi:10.1186/1743-7075-3-2
Kris-Etherton PM, Keen CL: Evidence that the antioxidant flavonoids in tea and cocoa are beneficial for cardiovascular health. Curr Opin Lipidol 2002, 13(1):41-49
The most extensively consistent finding is the association between chocolate flavonoid intake and CHD mortality.
Hertog MG, Kromhout D, Aravanis C, Blackburn H, Buzina R, Fidanza F, Giampaoli S, Jansen A, Menotti A, Nedeljkovic S, et : Flavonoid intake and long-term risk of coronary heart disease and cancer in the seven countries study. Arch Intern Med 1995, 155(4):381-386.
Geleijnse JM, Launer LJ, Van der Kuip DA, Hofman A, Witteman JC: Inverse association of tea and flavonoid intakes with incident myocardial infarction: the Rotterdam Study. Am J Clin Nutr 2002, 75(5):880-886. [PubMed Abstract]
Rimm EB, Katan MB, Ascherio A, Stampfer MJ, Willett WC: Relation between Intake of Flavonoids and Risk for Coronary Heart Disease in Male Health Professionals. Ann Intern Med 1996, 125(5):384-389. [PubMed Abstract]
Sesso HD, Gaziano JM, Liu S, Buring JE: Flavonoid intake and the risk of cardiovascular disease in women. Am J Clin Nutr 2003, 77(6):1400-1408. [PubMed Abstract]
Hertog MG, Feskens EJ, Hollman PC, Katan MB, Kromhout D: Dietary antioxidant flavonoids and risk of coronary heart disease: the Zutphen Elderly Study. Lancet 1993, 342(8878):1007-1011.
Hirvonen T, Pietinen P, Virtanen M, Ovaskainen ML, Hakkinen S, Albanes D, Virtamo J: Intake of flavonols and flavones and risk of coronary heart disease in male smokers. Epidemiology 2001, 12(1):62-67. [PubMed Abstract] [Publisher Full Text]
Keli SO, Hertog MG, Feskens EJ, Kromhout D: Dietary flavonoids, antioxidant vitamins, and incidence of stroke: the Zutphen study. Arch Intern Med 1996, 156(6):637-642.
Arts IC, Jacobs DRJ, Harnack LJ, Gross M, Folsom AR: Dietary catechins in relation to coronary heart disease death among postmenopausal women. Epidemiology 2001, 12(6):668-675. text:  
Yochum L, Kushi LH, Meyer K, Folsom AR: Dietary flavonoid intake and risk of cardiovascular disease in postmenopausal women. Am J Epidemiol 1999, 149(10):943-949.
Knekt P, Jarvinen R, Reunanen A, Maatela J: Flavonoid intake and coronary mortality in Finland: a cohort study. BMJ 1996, 312(7029):478-481.
Knekt P, Kumpulainen J, Jarvinen R, Rissanen H, Heliovaara M, Reunanen A, Hakulinen T, Aromaa A: Flavonoid intake and risk of chronic diseases. Am J Clin Nutr 2002, 76(3):560-568.
Short-term administration of dark chocolate is followed by a significant increase in insulin sensitivity and a decrease in blood pressure in healthy persons -- Grassi et al. 81 (3): 611 -- American Journal of Clinical Nutrition, Vol. 81, No. 3, 611-614, March 2005
Grassi D, Necozione S, Lippi C, Croce G, Valeri L, Pasqualetti P, Desideri G, Blumberg JB, Ferri C: Cocoa Reduces Blood Pressure and Insulin Resistance and Improves Endothelium-Dependent Vasodilation in Hypertensives. Hypertension 2005, 01.HYP.0000174990.46027.70.
Taubert D, Berkels R, Roesen R, Klaus W: Chocolate and blood pressure in elderly individuals with isolated systolic hypertension. JAMA 2003, 290(8):1029-1030.
In addition to anti-inflammatory effects on the lipoxygenase pathway, cocoa polyphenols have been shown to decrease inflammation via several mechanisms, namely: inhibition of mitogen induced activation of T cells, polyclonal activation of B cells, reduced expression of interleukin-2 (IL-2) messenger RNA, and reduced secretion of IL-2 by T cells – all these are inflammatopry markers. Other studies have also found chocolate procyanidins can modulate of a variety of other cytokines (e.g. IL-5, TNF-a, TGF-ß), reducing their inflammatory effects [110-114].
Helmut Sies, Tankred Schewe, Christian Heiss and Malte Kelm. Cocoa polyphenols and inflammatory mediators, American Journal of Clinical Nutrition, Vol. 81, No. 1, 304S-312S, January 2005
Sanbongi C, Suzuki N, Sakane T: Polyphenols in chocolate, which have antioxidant activity, modulate immune functions in humans in vitro. Cell Immunol 1997, 177(2):129-136.
Mao TK, Powell J, Van de Water J, Keen CL, Schmitz HH, Hammerstone JF, Gershwin ME: The effect of cocoa procyanidins on the transcription and secretion of interleukin 1 beta in peripheral blood mononuclear cells. Life Sci 2000, 66(15):1377-1386.
Mao T, Van De Water J, Keen CL, Schmitz HH, Gershwin ME: Cocoa procyanidins and human cytokine transcription and secretion. J Nutr 2000, 130(8S Suppl):2093S-9S.
Mao TK, Van de Water J, Keen CL, Schmitz HH, Gershwin ME: Effect of cocoa flavanols and their related oligomers on the secretion of interleukin-5 in peripheral blood mononuclear cells. J Med Food 2002, 5(1):17-22.
Mao TK, van de Water J, Keen CL, Schmitz HH, Gershwin ME: Modulation of TNF-alpha secretion in peripheral blood mononuclear cells by cocoa flavanols and procyanidins. Dev Immunol 2002, 9(3):135-141.
Mao TK, Van De Water J, Keen CL, Schmitz HH, Gershwin ME: Cocoa flavonols and procyanidins promote transforming growth factor-beta1 homeostasis in peripheral blood mononuclear cells. Exp Biol Med (Maywood) 2003, 228(1):93-99.
Multiple cocoa feeding trials have also found chocolate to increase HDL (good) cholesterol and lowers LDL (bad) cholesterol.
Mursu J, Voutilainen S, Nurmi T, Rissanen TH, Virtanen JK, Kaikkonen J, Nyyssonen K, Salonen JT: Dark Chocolate Consumption Increases HDL Cholesterol Concentration and Chocolate Fatty Acids May Inhibit Lipid Peroxidation in Healthy Humans. Free Radic Biol Med 2004, 37(9):1351-1359.
Mathur S, Devaraj S, Grundy SM, Jialal I: Cocoa products decrease low density lipoprotein oxidative susceptibility but do not affect biomarkers of inflammation in humans. J Nutr 2002, 132(12):3663-3667.
Wan Y, Vinson JA, Etherton TD, Proch J, Lazarus SA, Kris-Etherton PM: Effects of cocoa powder and dark chocolate on LDL oxidative susceptibility and prostaglandin concentrations in humans. Am J Clin Nutr 2001, 74(5):596-602.
Professor of metabolic physiology at Nottingham University, Ian Macdonald, used MRI technology (magnetic resonance imaging) to monitor greater activity in particular areas of the brain in people who had ingested a cocoa drink, rich in flavonols.
Reported at the 2006 American Association for the Advancement of Science (AAAS)
Subjects had a doubling of blood flow in the skin in tissue 1 millimeter below the surface, and a 37.5 percent increase in tissue 7 to 8 mm deep.
Hurst WJ, Martin RA, Zoumas, BL. Biogenic amines in chocolate: a review. Nutr Rep Intl. 1982;26:1081-6.
(Ada) Zurer, P. 1996. Chocolate may mimic marijuana in brain. Chemical and Engineering News 74(Sept. 2):31 also: Brain Cannabinoids in Chocolate, Nature, August 22, 1996, pp. 677-678 by diTomaso, E., Beltramo, M., and Piomelli, D.
In this socioeconomically homogenous male study cohort, chocolate preference in old age was associated with better health, optimism and better psychological well-being.
European Journal of Clinical Nutrition advance online publication, 28 February 2007; doi:10.1038/sj.ejcn.1602707. Eur J Clin Nutr. 2007 Feb 28
Lee IM, Paffenbarger RSJ: Life is sweet: candy consumption and longevity. BMJ 1998, 317(7174):1683-1684.
L-theanine is a unique free form amino acid found only in the tea plant and in the mushrooms Xerocomus badius and certain species of genus Camellia, C. japonica and C. sasanqua.
In a study of the role of theanine in mitigating the effects of premenstrual syndrome (PMS), 20 women were administered Suntheanine 100 mg twice a day (200 mg) or placebo, through three menstruation cycles. Theanine significantly reduced scores on both physical and mental symptoms of PMS.
Ueda T, M Ozeki, T Okubo, D Chu, LR Juneja, H Yokogoshi, S Matsumoto. 2001. Improving effect of L-theanine on premenstrual syndrome. J JSPOG 6:234-239. [English Abstract]
L-theanine appears to have a role in the formation of the inhibitory neurotransmitter Gamma Amino Butyric Acid (GABA). GABA blocks release of the neurotransmitters dopamine and serotonin, playing a key role in the relaxation effect.
GABA, or gamma-aminobutyric acid, is a messenger chemical that is essential for optimizing how brain cells transmit messages to each other and acts to put a damper on unwanted brain signaling activity, explained the study's lead author Dr. Audie G. Leventhal at the University of Utah School of Medicine in Salt Lake City.
Kimura K, Ozeki M, Juneja L, Ohira H (2007). "L-Theanine reduces psychological and physiological stress responses". Biol Psychol 74 (1): 39–45. doi:10.1016/j.biopsycho. 2006.06.006. PMID 16930802.
Haskell CF, Kennedy DO, Milne AL, Wesnes KA, Scholey AB (2008). "The effects of l-theanine, caffeine and their combination on cognition and mood". Biol Psychol 77 (2): 113–22.
Alpha waves are associated with a relaxes, dreamy (but not trance-like) state, helpful for sports performance. Relaxation is also a way of beating fatigue (less beta waves, less stress and anxiety).
Kobayashi K, Y Nagao, N Aoi, LR Juneja, M Kim, T Yamamoto, S Sugimoto. 1998. Effects of L-theanine on the release of alpha-waves in human volunteers. Nippon Nogeikagaku Kaishi 72: 153-1 57.
Juneja LR, Chu D-C, Okubo T, Nagato Y, Yokogoshi H. L-theanine-a unique amino acid of green tea and its relaxation effect in humans. Trends Food Sci Technol . 1999;10:199-204.
Song et al. (2002) performed a randomized placebo-controlled double-blind crossover study with 20 subjects age 30-55 years suffering from persistent fatigue. The subjects were classified as high or low in anxiety. Each subject’s frontal and occipital EEG was measured over 1 hour immediately after the administration of a placebo or 200 mg L-theanine every day for 7 days. The subjects were also evaluated on the Fatigue Severity Scale. Both endpoints showed significant relaxant effects of theanine; the fatigue score was significantly decreased in the test group but not in the placebo group.
Song CH, KI Chung, SW Song, KS Kim. 2002. The effects of L-theanine containing functional beverage on mental relaxation and fatigue perception. J Korean Acad Fam Med 23:645.
Kobayashi et al. (1998) divided 50 females age 18-22 into a high-anxiety group and a low-anxiety group based on scores on the Manifest Anxiety Scale. Subjects were given either 50 mg or 200 mg theanine in water once a week. Each subject’s electroencephalogram (EEG) was taken for 60 minutes after each administration. Effects were observed beginning about 30-40 minutes after intake, taking the form of increased production of alpha waves (reported to be characteristic of relaxation), but not theta waves (reported to be indicators of drowsiness).
L-theanine is considered to be safe based on its historical use as a component of tea and on favorable toxicology studies. Tea is the most consumed beverage worldwide after water, and has been consumed for thousands of years by billions of people. It is estimated that a heavy tea drinker (6-8 cups daily) will consume between 200 to 400 mg of L-theanine daily.
A 'letter of no objection' from the US Food and Drug Administration (FDA) for the self-affirmed GRAS status of its L-theanine brand Suntheanine.