I'm pretty sure that any class\race combo would work (assuming that the race in question wasn't something that would draw attention to itself by virtue of rarity in your world).
The hardest would be paladins and antipaladins due to the aura class feature. Monks and Cavaliers could also have a hard time due to alignment and order restrictions. I think any class with casting would do fine.
The trick to a character working in such a campaign is to be very clear what you are going for and the kind of skills that will help them - and to encourage the group to pick complimentary skills ('bob is our lock picker - and katy is our backup and on tough locks she helps bob').
The rogue is allegedly a stealth based character.
Besides +3 as a class skill (which is available for a trait) what stealth based features does it actually have?
Bards and inquisitors. They have the skill points and spells to sneak around, fool people, and most importantly, hide their alignment. That said inquisitors need to be a specific archetype. Those on the wizard spell lists can also work decently enough.
Almost anything can play the part provided it keeps its ACP low and has enough skill points to be well-rounded on the skill front. Spellcasting or UMD is also extremely beneficial since there are a lot of very useful effects you can only get with magic, and to an extent can make up for bad skill options on classes like the Sorcerer. Stealth as a class skill can always be picked up as a trait, and almost every class has something useful to offer to these kinds of campaigns. Even the Fighter isn't completely out of the picture, though it's still a very challenging class to play in a campaign like this even with careful archetype and feat selection to make him more well-rounded.
I think monks and cavaliers could work, and Paladins or Antipaladins could work depending on the alignment of the organizations. That is going to be the main thing to determine alignment restricted classes. For the characters' network, npcs that are rogues and the like would be the best flavor wise, but enforcers and that kind of thing are always there as well and they can be nearly any class.
Well depending on the character and the desire to use vows - between monk vows, cavalier orders, and paladin/anti codes those 4 classes would have the hardest time - while there are archtypes that fit a campaign like this for every class, most of the other classes could make almost any of them work. The paladin and anti-paladin specifically would need an archtype from the new intrigue book to work in a campaign like this without running into issues.
I think an investigator would work rather well in a stealth/ espionage campaign. Lots of skills, trap disarming, can hold his own in short melees, Insperation to key skills at key moments.
One question:
There is the Magus the class mixture between wizard and fighter, there aren't similar class but the mix between rogue and wizard?
I know there is the Arcane Trikster, but I dosn't like it very much.
I very like the sneak attack and the spellcasting.
Any suggestion?
The Eldritch Scoundrel and Sandman Bard would be your only other good options for arcane spellcasting + sneak attack.
Suggest the party all take the stealth synergy feat.
We have in our current Skull & Shackles game and it really opens up a lot more possibilities for sneaky activities because the whole party can creep in and out of places instead of most people waiting will the rogue or the invisible wizard does a solo section.
Suggestion about class with a similar concept?
A sneaky caster able to infiltrate enemy camp with invisibility or magic and able to cast mind controlling spells to make the foes fight between themselves.
Like Skyrim's frenzy: http://elderscrolls.wikia.com/wiki/Frenzy_(Skyrim)
and able to avoid combat.
Most corresponds to mesmerist. With Cunning caster feat.
IMO the huge advantage of URogue is Skill Unlock.
When you get Skill Unlock stealth you get to snipe at -10, instead of -20.
If you combine that with Halfling Racial Trait, you get another -10, so basically you're sniping at -20.
That would be great for killing enemies at distance without being noticed.
Otherwise, a 6th Spell class will do the trick. Combine Stealth+Spells and you're pretty much safe.
If you REALLY want to be good, I'd take somehow a Bat Familiar, which has Blindsense 20ft, which will help you detect enemies in case you fail, if it's dark or whatever.