I followed tennis very closely in the 90s(more than most posting here I suspect), and have probably written thousands of words over my many years here on many of the players mentioned so far, so I'm not sure where to begin. Was reluctant to post about this stuff again because of the effort required.
Also I see that the OP is talking about 1989-2004, so I will be mentioning players from there as well.
I value peak play pretty highly so I would rank Courier highly. In the 90s, upsets were an epidemic on all surfaces, especially clay, so seeing Courier breeze through the titles at Rome and Paris was pretty shocking, I certainly didn't see that coming. And he destroyed Muster in the 2nd round of Paris(beat him in Rome also) and Muster won Monte Carlo that year so these results are telling. And he destroyed Mancini as well(the best player on clay from 1989) and the young sensation of the tournament - Medvedev.
Courier was up a break in the fifth set of 93 Paris, so he was close to a very significant achievement at the time - 3 straight French Opens, a pretty small group of players.
bruguera's win in 93 was one of the most significant major wins of the open era, imo. His win/loss on all other surfaces at the time was less than .500, I remember Mac being blown away by that stat when he was calling the match.
A true claycourt specialist had never won the French before and bruguera qualified(though he eventually became good on all surfaces)
I had seen so many claycourters up until that point have great clay seasons then come to the French and lose to the top players like Lendl or Wilander or even Edberg(beat Mancini in 89) and Young Agassi(beat Perez roldan in 88) so bruguera delivering on his clay promise was big.
Also his peak level was pretty high as well imo. His game wasn't as offensive oriented as courier or Kuerten but when he was on it was hard to stop. And he could handle S&V players that were hot much better than muster(we all know muster's shock results in Paris over the years)
Bruguera's win over Medvedev in 94 RG was very impressive, Medvedev had won Monte Carlo and Hamburg that year. And his win over Berasategui was pretty impressive as well, he made the final without dropping a set(the only unseeded player to ever do that) and was hitting a ridiculous amount of fh winners, but bruguera was able to negate that weapon. Bruguera had an interesting style, most think of him as a human backboard, which he was to a degree, but he yet didn't have super human fitness like muster or courier. Had great passing shots and touch. Shades of Orantes in his game. His match with Becker in 91 Monte Carlo is one of the most entertaining claycourt matches I've seen.
I'll try to post more later, but to address
@Waspsting question.
I posted some of this in response to gary in another thread. There are many reasons why there was so much inconsistency of claycourters in the 90s and why top players are incredibly consistent on clay today.
First top players today are incredibly consistent on all surfaces. We see the same players in the 2nd week of Wimbledon as the French and this has been happening for years. And it's not just the big four, guys like berdych, Ferrer, tsonga and others have had very good results on grass and clay. This sort of thing just didn't happen in the 90s on a consistent basis. Partly why Agassis career slam was such a big deal, I felt like I was watching a historic thing that may not happen again for many years.
Basically today's players play hardcourt tennis year round whether it be on clay or grass. Yeah I know there are adjustments but they arent dramatic adjustments. Nadal is a great claycourter, but he plays nothing like a bruguera or muster, hits more fh winners in a week than they hit in months. And pretty much all his points are played under 5 shots. While a bruguera berasategui match has ridiculously long rallies.
Other factors - there were unbalanced draws in the 90s on clay. I mentioned muster vs courier in 2nd round of 92 RG, when both won clay masters that year. In 98 Rios played Costa in 4th round, both had masters that year. Winner played Moya, another masters winners. Year after year you had great claycourters play each other in early rounds of French. Often the best clay courters werent even in the top 10.
Another factor of why they were inconsistent - injuries. Clay was such a physical game, the good clay courters often just had one or two good years before their body broke down. The idea of a RG final with two 30 year olds like we had this year would have been beyond absurd to me circa 1997. There were usually only two 30 year olds in the entire top 100 back then. there were multiple years in the 90s where every quarterfinalist was under 24. It was sort of the norm. Now the norm is almost everyone being 28 and over. Since top players today are having almost unprecedented longevity, it makes sense they would have higher win percentages as well I think.