I actually wished I could use Prestige Classes more (big fan of them since the 3.5e days) but they are usually either too weak or they do not fit the character concept I am going with for that given character. Sometimes the former, sometimes the latter, usually a mix of both.
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The PC prestige classes that I have played, or someone in my group has played are:
Holy Vindicator - twice - 1 in Rise of the Runelords and 1 in Wrath of the Righteous
Horizon Walker - Wrath of the Righteous
Riftwarden - Wrath of the Righteous
Master Chymist - about to add to my ragechemist in Shattered Star
I also had a character planning to go Loremaster in a PBP that died.
Assassins are outclassed by Slayers.
Assassins have a lower BAB but more sneak attack damage dice, so this isn't true.
Eldritch knights aren't as good as Magi.
Also not true. Eldritch Knight's strength relies on its ability to have a BAB of +15 (same as the Magus) as well as 9th level spellcasting. The magus is better at doing damage, but the Eldritch Knight is better at being a wizard who casts spells.
[quotes]Lion Blades are just laughable even compared to a properly archetyped rogue which is just awful.
Isn't the Lion Blade a three level prestige class?
Most of the decent prestige classes are holdovers from 3.5 which favored prestige a lot more.
Not true. Paths of Prestige has some awesome Prestige Classes, both the Golden Legionnaire and the Shield Marshal both come to mind. Gray Gardener is pretty good too.
Paizo seems to prefer people staying in their class without multiclassing or prestiging. I like this philosophy but others chafe under it.
Single classing builds are better for general builds, multiclassing is superior for specialized builds. The Golden Legionnaire drops much of the fighter's flexibility for party buffing, for instance. It is a beast at martial, all-day buffing.
Master Chymist is covered in all of the Alchemist guides; since Alchemists are the only class that can qualify, there's no real reason for it to have a guide of it's own.
It's fairly popular, and (at least as a 3 level dip, if not a full 10 levels), very strong.
i played 1 master chymist back in 2011, and had a grand time, but as noted its advice is under alchemist guides, and its only useful if you intend to become a front line combatant, really. (A little use with "mad bomber" builds but mainly for "mr. Hydes".)
My alchemist eventually died to the Crimson Throne AP, but the roleplaying aspects of someone who can't control the results of their dangerous experimentation with alchemy is fantastic. ;)
Prestige classes my group's done in Pathfinder games..
Arcane trickster (3 times; the most recent is a wizard (spellslinger)/rogue (sniper) in a mythic campaign, so archmage arcane trickster with a musket; he just started the PrC)
Magaambyan Arcanist (it's a fun PrC, and I'll cheerfully recommend it; I combined it with playing a samsaran with mystic past life to also get a bunch of spells off the witch list, so between that and the PrC my wizard had stuff like barkskin, commune with nature, death ward, freedom of movement, holy word, heal, resurrection and atonement; it was neat).
Mystic Theurge (druid/empyreal bloodline sorcerer, for extra weirdness)
Jade Phoenix (Tome of Battle PrC, modified to work with DSP psionics instead of arcane casting)
Eldritch Knight (2 of these; the most recent is in my RotRL game)
Oh, as to Pathfinder Chronicler. One of the Serpent's Skull NPCs has that PrC. It actually makes for a really nice support character if you advance it far enough.
Archetypes (including homebrew ones) get used pretty frequently in our games (hell, in the game with the arcane trickster gunner mentioned above, every single PC is using an archetype). Prestige classes see far less use in our Pathfinder games than they did under 3.X, largely as a result of the 1-20 classes being much better now. We've seen at most 2 PCs with a prestige class in one game.
(Under 3.X, the norm was every single character having a prestige class.)
I'd like to play a cavalier/hellknight, but I don't know when that character's happening.
I've played a Witch/Harrower and a Dervish Dancer Bard/Shadow Dancer - both fun combinations.
In games I've had two people use duelist (one bard/duelist, the other a rogue/fighter/duelist). We also have a Paladin/Hellknight in Crimson Throne.
In upcoming games there will be a dragon disciple and a veiled illusionist tried out.