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 .
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This could be the Stainless Steel Rat series, by Harry Harrison.
Those are very openly comic stories about James Bolivar DiGriz.
He is a 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.
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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 Lilith:
A Snake in the Grass (1981) Cerberus:
A Wolf in the Fold (1982) Charon: A Dragon at the Gate (1982) Medusa: A Tiger by the Tail (1983)
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Could be Tuf Voyaging Haviland Tuf has a "seedship" and travels around and tries to help different worlds, at a cost.
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This feels like the Death Gate cycle , where the first four books fit the theme of travelling between worlds (via magical gates rather than interstellar ships) and influencing the peoples there.
One world even involved a kind of communist uprising.
The latter books then tie the worlds together for a larger story.
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Could it be E. C. Tubb's Dumarest saga?
The lead character is looking for Earth, and each book ends up on a new planet having adventures.
The first one is The Winds of Gath .
Wikipedia notes:
Gath is a world with a unique tourist attraction: a mountain-sized white noise amplifier.
With no indigenous economy other than the tourist slave labor trade, Dumarest struggles to break free from this dead-end world.
Dumarest becomes attached to the retinue of the Matriarch of Kund and unwittingly finds himself embroiled in the vicious and complex political intrigues of the Matriarch's court.
After some keen detective work from Dumarest and the ensuing deadly battle with the Cyclan, Dumarest prevails and escapes from the backwater planet.
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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.
Science fiction series where in each novel, a man travels from planet to planet and helps the inhabitants in overthrowing their oppressors
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It is not clear exaclty which book the question refers to, but there are several possibilities. The Rogue Wizard series by Christopher Stasheff features a similar storyline. Similarly, The Stainless Steel Rat series by Harry Harrison and the Death Gate cycle also have plots like this. There are a number of possibilities, including Christopher Stasheff's Rogue Wizard series, Harry Harrison's Stainless Steel Rat series and E. C. Tubb's Dumarest saga.
It could be Christopher Stasheff's Rogue Wizard series. There are 10 books in which the hero wonders the galaxy protecting the innocent and ooverthrowing oppressors. It could be Harry Harrison's Stainless Steel Rat series, openly comic novels which follow the escapades of super-spy James Bolivar DiGriz. It could be Tuf Voyaging in which Haviland Tuf has a "seedship" and travels around and tries to help different worlds, at a cost. It could be the Death Gate cycle, where the first four books fit the theme of travelling between worlds (via magical gates rather than interstellar ships) and influencing the peoples there. It could it be E. C. Tubb's Dumarest saga, where the lead character is looking for Earth and ends up on a new planet in each book.