In my opinion, all perstige classes are kind of lame.
As modular as 3.5e is, I always figured most of what is trying to be achieved by a prestige class could be done just as well with a series of feats and/or multiclassing then another type of class. To me the whole Prestige Class mechanic was invented to both satisfy power-gamers and sell more books.
I've never used a PrC as a player because I've done everything I could want with core class combinations. The only concept you can't do with core D&D classes is a divine spellcaster that isn't a master of whupass. I find it odd that in most published settings a cleric of a deity of a non-martial deity would still be trained in the use of armor and have a favored weapon. "The Goddess of Eternal Peace, Love, and Fluffy Pillows preaches that if an enemy strikes you, turn the other cheek. Unless he's Chaotic Evil, in that case, KILL THE BASTARD!" But I digress.
Want to make an Assasin like the PrC? Make a Rogue with a couple of levels of Sorceror for the spells, maybe some levels in Fighter if you want to use more weapons or fight a little better. Poison use and Death attack can be add-on feats with appropriate prerequisites.
As a DM, I don't allow PrC's in general (then again, I perfer to DM Grim Tales or True 20, so it doesn't come up that often anyway). In part this is out of laziness: I don't want to keep up with even MORE classes. Plus I just don't like the idea that every single thing about a character HAS to have a statistical benefit.
For instance, if you join an elite order of a priesthood, I'd much rather roleplay it and have other in-game benefits. The character has powerful connections and access to the order's resources, plus bearing the sign of the order makes the character more credible to people in the kingdom. The flashy new robes are a plus as well...
For an assasin's guild, I'd have the player first try and find the guild (which may be an adventure in itself, especially if the character isn't too subltle about wanting to join a band of killers-for-hire). The guild would grant benefits like regular "work," as well as protection from the local authorities for sanctioned assasinations. The down-side would be having to swear absolute loyalty to the guild and having only one way to retire...
To me that's more interesting than another table of bonuses and some new class ability that basically transaltes to some new "kewl way to kill monzterz" that mechanically isn't much different than all the other ways to inflict mayhem already in the standard rules.