One of my favorite examples is Jean-Francois de Galaup, Comte de la Pérouse, who set out with two converted merchantmen, La Boussole and L'Astrolabe in 1785 to explore the Pacific Ocean with 225 crew, officers and scientists. The expedition sent regular reports back to France, sailed through the Pacific Northwest and Southeast Alaska, traveled to Hawaii, China, Sakhalin Island, the Philippines, and down to Australia. In 1788, the two ships stopped at Botany Bay in Australia. After they sailed out of Botany Bay, they promptly disappeared, and all aboard the expedition were killed.

As sad as the disappearance is, that doesn't answer your question. The La Pérouse expedition was conducted at the height of the Enlightenment and was created with an eye to fixing the problems that Capt. Cook had encountered when he sailed through the Pacific. La Pérouse had a record of humanitarianism (exhibited during the frequent French wars with Britain) and was selected because of that record. He deliberately chose converted merchantmen instead of warships and took only the bare minimum of weaponry needed to provide security.

Competition to be aboard the expedition was fierce, with applications from across France. One of those who applied was a 16-year-old Corsican named Napoleon Bonaparte.

La Pérouse's ships were packed with trade goods and scientific instrumentation. When he arrived in Alaska with his ships in need of repair, he traded with the Tlingit natives for use of their forest. He didn't simply go ashore and take water and timber as was par for the course at the time. The contemporary view was that land laying idle was open to anyone; la Pérouse had a strikingly modern conception that territory belonged to its inhabitants until proven otherwise. He wasn't perfect by any means -- there were mistakes along the way, but they were mistakes of mistranslation and misunderstanding. In 1980, Carl Sagan compared la Pérouse's encounter with the Tlingits to the Spanish conquest of the Aztecs during the final episode of Cosmos.

La Pérouse's expedition was famed throughout France during the years immediately before the French Revolution. This was the equivalent of a space program for France: The nation had funded a scientific expedition into the unknown, and there was no telling what it would find. The expedition's disappearance was a tragedy. The two ships had wrecked off the island of Vanikoro, marooning the expedition's survivors, who lived for some years longer before dying. A rescue mission was launched in 1791 but found no trace of the expedition. The rescue mission returned home, disappointed, two years later, just as King Louis XVI was about to be executed.

As he was led to the guillotine, some of King Louis XVI's final words were, "What news of La Pérouse?”

Zheng He. Sailing from Ming China sometime in the mid 15th century, he sailed as far as Zanzibar and visited Persia, India, Ceylon and a few others along the way.

Not only did Zheng He not bother with subjugation or invasion, he actually went out of his way to be tolerant and respectful of other cultures. When asked to make a good luck note in a very important religious shrine in Sri Lanka, he (A Hui Muslim) didn't just thank Allah, but also recorded his giving of thanks to the Buddha, in Chinese, Persian and Tamil (an Indian language.) So that anyone visiting would understand how important the Buddha was. (Despite not being Buddhist at all.)

So this was almost 50 years before the Europeans trotted off to the new world to get filthy rich, and yet Zheng He was exhibiting a weird amount of tolerance and respect, and refused to subjugate anyone he visited along the way. In fact, this was what nearly all Chinese explorers did.

China is incredibly different to Europe in many ways.

This is a piggy-back question, but I've often heard of explorers like James Cook and Samuel de Champlain having good reputations in regards to this topic. Can anyone write a bit about them?

Samuel Champlain has frequently been mentioned in modern accounts as more tolerant of native cultural practices than many of his contemporaries. He is certainly depicted this way in Champlain's Dream by David Hackett Fischer.