Critics of Tolkien have claimed his works to racist against black, Arabs, Asians, etc, and to have similarities to Nazi ideas, but Tolkien himself vehemently denies this. Although his works may contain some taint of the racism found in European culture, Tolkien was strongly opposed to racism. His works are far less racist than most from his time.
I too think Elves and men may be considered the same species biologically. The difference between their bodies is a result of them possessing different types of souls, and to the elves having more direct knowledge of the Valar (The greater hight and beauty of the Elves is due to their association with the Ainur. Those who spent time in the uttermost west or with Thingol's wife (a Maia) are said to have grown significantly taller, fairer, and wiser.) Both the Eldar and the Edain are the Children of Illuvatar. Elves and men clearly can crossbreed, as can their offspring. It is often difficult to tell them apart based on physical appearance.
The Silmarilion make it clear that the Elven soul is immortal in this world, but will cease to exist when the world ends. It also states that the Elves were once far more like humans (as are younger elves), but that over time they become less like men because their bodies are supernaturally sustained by their souls. Tolkien's elves actually remind me a lot of the Sidar, although they were created to be "shades" and did not rely on sorcery to gain their immortality. Also, If their spirits are weakened due to depression they can lose the ability to sustain themselves such, and their bodies succumb to the laws of nature and age, grow sick, and even die just like the bodies of men. The Human soul is different; it isn't designed for this world. It is made has a deep desire for thing this world cannot provide, and to have this desire fulfilled when, upon death, the soul leaves Ea. Not even the Valar know for sure, but it is believed that the soul of men leave the world to meet Illutatar himself, and that they will truly live on forever and take part in the creation of a new and better earth. Men were made to be the "gods" of the world to come.
The souls of Men are also given greater free will than the souls of the Elves. The Elves and even the Valar are constrained to only act according to the Music of the Ainur which they created before the creation of the world (although they, especially in the case of Melkor, may not realize or intend their actions to have these consequences). Men are free from Fate. Illuvatar freely gave them the power that Melkor always wanted: the right to make the world what they wanted it to be, not bound even by the will and plans of The One. (Elves and sometimes even the Valar look down on men for their disregard for fate, thinking it makes us just like Melkor. However, Illuvatar himself elected to make men rebellious by nature, so this is not in fact a sign of corruption but of our original intent.
Orks were corrupted elves. (However, Tolkien is said not to have liked this idea, and later tried to change it to make them corrupted men. It is also possible that some are corrupted men, some are corrupted elves, some are crossbreed of the two, and a few of the strongest may actually be fallen Maiar.) The fact that they are described as shorter and uglier than men while elves are taller and fairer is a result of them being corrupted by evil instead of enlightened by good. (It could also indicate that the original elven stature is intermediate between these two, i.e., the same as human stature.) Orks and golblins are the same, with the terms often but rather inconsistently used to describe different types of orks. It is possible that the different types may have originated from different races. Although they are very corrupted, they aren't pure evil. They only serve evil out of fear. They are redeemable.
Dwarves were created by Aule when he got impatient of waiting for the Children of Illuvatar. He was confromted by Illuvatar and chastised for creating being that could never be more than slaves, as only The One had the power to create a soul. He repented and almost destroyed the dwarves, but Illuvatar forgave him and granted souls to the Dwarves, provided the Dwarves not be brought to life until after the Firstborn. No one really knows what the dwarven soul in like, whether it is the same as a Human or elven one or totally different. Dwarves live far longer than men, but are not by any means immortal. The custom of reusing names has led many to believe the Dwarves believe their souls are reincarnated into their descendants. (One group of Dwarves, the petty dwarves went extinct long ago. These were smaller than most dwarves, and I think I recall that they had less facial hair but more body hair. They were the first Dwarves to move east. The Elves didn't recognize them as a sapient species, and hunted them for food. This led to their extinction (although the last petty dwarf was killed by a Man, not an Elf, iirc))
Aule's wife (Yovanna? the Valie of nature) was upset with him for creating Dwarves, and though that since she had no part in their creation they would be hostile to nature, destroying the trees (she was right). Thus, she created the Ents to guard them. They too were granted souls by Illuvatar.
Trolls are the only life that Melkor created on his own in stead of corrupted. The made these as mockeries of the Ents. Unlike the Ents, these did not have souls. Any semblance of intelligence in them comes from Melkor (or latter, Sauron). They don't have any free will.
I'm not sure about Hobbits. Halflings are said to be closer relatives of men than are the Elves or even the Dwarves. They are likely just a "subspecies" that evolved from men. A few places seem like they might imply that some may be related to dwarves. Perhaps they are a men crossbred with with dwarves (or maybe with Petty Dwarves, since I believe hobbits were said to be smaller than dwarves)?