I'm considering letting a player use a savage progression from one of the aforementioned mags, but I know they were 3.5. How would you fairly convert any of these to Pathfinder, considering how much more powerful PF classes are than equivalent 3.5?
Monster classes were always subpar compared to PC classes.
The 3.5 Monster progressions are based on HD+LA=ECL.
So, for example, the 3.5 Minotaur has 6 racial HD, plus a LA +2, for total ECL of 8. So a Monster progression for the Minotaur should be 8 levels long.
But in Pathfinder, a monster is ECL = CR, going on the Monsters as PCs rules.
So the Pathfinder Minotaur has 6 racial HD, but its ECL is only 4. So the Pathfinder monster progression should only be 4 levels long.
The extra racial HD (and the hp, BAB, and Saves from them) help make up for the fact you don't have any class abilities for these HD.
It may be easier to just write a new progression. But if you think it would save you time, compare the 3.5 ECL with the Pathfinder ECL. Then, when leveling up the PC, they could "level up" multiple levels of the 3.5 Monster progression at each new level, so that it only takes the number of levels it should for Pathfinder.
For example, if you were playing the aforementioned Minotaur, each time the PC gains a level they would gain 2 3.5 monster progression levels. Because the 3.5 progression is 8 levels long, but the PF ECL is only 4.
Sometimes the math doesn't work out evenly. Take the Satyr, 3.5 ECL is 7 (5HD +2LA) but the PF ECL is 4 (CR 4). I would let the PC gain 2 monster progression levels at 1st, 2nd, and 3rd levels, then one level at 4th.
You also need to make sure the skills, BAB, and abilities are all converted to PF (check for any changes in the Type features and traits).
That is all a lot of work.
See also this thread.