Only voting for the four you mention, and adding Score to the mix, this is interesting. Many of the flagship sets were okay, but when including others produced by the companies (Donruss-Triple Play, Topps-Bowman, Upper Deck-Collector's Choice) that changes things a lot. At least for me it does.
1. Score- Sentimental but 1994 Score is my favorite set of all time, even the Series two hockey set is one of my all time favorites and I don't think I currently own any.
2. Upper Deck- Mainly because of the Collector's Choice brand, which I had tons of. They also had great sets with the Victory and HoloGrFX brands.
3. Donruss- I loved the Triple Play brand so much growing up in the 90's. So much that I bought a couple boxes of 1992 and 1993 earlier this year. Hope to finish those sets as well as build the 1994 set as well. I liked the 90's flagship sets of Donruss so much more than than the 80's ones.
4. Topps- I always thought they had solid sets, but none outside of 1994 Topps ever WOW'ed me. I hated some of their 80's sets so that also knocks some points off. I never collected Bowman or Stadium Club much back then and honestly wasn't a fan anyways.
5. Fleer- Fleer had some really good stuff, but 1991 Fleer still gives me nightmares and Ultra never appealed to me either.
Having said all that, I would much rather see all these brands back as their own companies instead of two companies using several names and mass producing cards like today. I much preferred more companies mass producing cards so that way there's more of a chance to find something you like.
Royal Card Review is my blog if you feel like checking it out, thanks if you do!- royalcardreview.blogspot.com/
In the process of updating my collection so don't trust any of my lists right now.