Ftyjtk

I don't remember much but I do remember that each novel takes place on a new planet where there was usually some sort of social upheaval/revolution happening and he helps the inhabitants overthrow their oppressors.

I think that in the first book he was alone but then gains a companion in his travels.

I believe you are thinking of the Rogue Wizard series, by Christopher Stasheff. The timing is about right (1993-2001) although the original book in the series was written much earlier (1979).

The protagonist's real name is Magnus d'Armand but most of the time he goes by his pseudonym Gar Pike, in order to minimize the risk of his activities causing trouble for his family. As you say, he wanders the galaxy protecting the innocent and overthrowing oppressors. You might also remember his possession of various Psi powers, though he usually tries to avoid using them until it becomes absolutely necessary to do so.

In the first of the newer books, A Wizard in Absentia, Magnus is alone. This is a prequel and comes first in terms of the in-universe chronology. It is followed by the original A Wizard in Bedlam at the end of which he acquires a companion.

There are ten books in the series in all, and the storyline is concluded in The Warlock's Last Ride from the related Warlock of Gramarye series.

This could be the Stainless Steel Rat series, by Harry Harrison. Those are very openly comic stories about James Bolivar DiGriz, former thief and now intergalactic super-spy for the Special Corps. He starts off alone, but marries the villainess of the first novel and they become a team; their sons are also involved in some of the stories.

Jack Chalker's Four Lords of the Diamond series follows an agent whose mind is remotely implanted in a host assassin on each of four worlds of the Warden Diamond system. In each book his mission is to investigate and overthrow the Lord of that world. But each of his duplicates learns more about the corruption of the intergalactic government that he works for and each one deviates more and more from the mission. The books are

1. 
   Lilith: A Snake in the Grass (1981)


2. 
   Cerberus: A Wolf in the Fold (1982)


3. 
   Charon: A Dragon at the Gate (1982)


4. 
   Medusa: A Tiger by the Tail (1983)

Could be Tuf Voyaging

Haviland Tuf has a "seedship" and travels around and tries to help different worlds, at a cost.