FR has some prestige classes interesting for cleric rogues in "faiths and Pantheons" , the "Strifeleader" (Clerics of Cyric) does nicely in the fields of Sneak Damage (+3D6 total) and people manipulation and gets some pretty nice illusion spells added to his clerical spell list (including...Invisibility). on the downside, you loose three levels of caster ability, and have to have at least one or two level of rogue to qualify for the class, skillwise.
The "Techsmith" (Clerics of Gond ) should prove really devastating in the anti-lock, anti-trap and anti-construct department (including his trusty "gondsman" mine-houn..ahem, bodyguard to set of traps ).
And the "Goldeye" (Clerics of Waukeen) is pretty good at appraisal, bluffing and general negotitaion in return for only a few levels of casting
All get 4+Int bonus skillpoints, like the Arcane Trickster.
But, and that is decisive to me, ALL are strictly tied to their respective god's portfolio and active spheres of interest - which IMHO is _the_ decisive factor about any such cleric prestige class, "How does it further the deity's purpose ?"... Usually deities' do not fulfill player's favourite plan on the most effective multi-class combination possible, put try to further their own plans.
And, purely from a roleplaying point of view - most rogues tend to be selfish individuals, concerned more with their personal fate and well-being, taking pride in their personal skill and accomplishment by their own hand. Clerics on the other hand tie their fate and power to the will of another, higher being, acting for his/her glory (and maybe their own as well ), trusting in the power channeld through them, not their own skill to accomplish their missions.
These two diverging attitudes do not get along all that well, except for some very few sneaky or eccentric gods, who like their clerics to act as they themselves would. And while a player could certainly rationalize how a rogue could serve Helm, god of guardians, Helm does not seem to feel it necessary to endow a possible PrC serving him with any special powers.
Which is my take, on just why none such general prestige-class exists.
Oh, and btw the FR-god of thieves and sneakiness, Mask does have his own special way of rewarding his faithful thieving servants, by making them resemble himself more, instead of giving them clerical powers. Admittedly, the Shadowmasters of Telflamm _are_ a scary bunch of people even without going cleric all the way - but it shows how god's go about settling and furthering their own portfolio. Mask wants people to worship secrecy, wit and stealth, not battling down the guards while channeling some righteous might.
