Bear these points in mind:
1 - By having Rogue levels, you trade off spellpower for physical capabilities. So your spells should be chosen with those capabilities in mind. If you have an amazingly high Hide check, don't choose Invisibility, which would make Hide obsolete. Choose Cat's Grace, which bumps Hide even higher, as well as other Dex-based needs.
2 - If you choose rapier as a melee weapon, you should really get the combo keen edge + magic (or greater magic) weapon+true strike, and probably invest on Improved Critical feat. Why? Rapier has a threat range of 18-20. With keen edge, it gets up to 15-20. Throw in Improved Critical and you're scoring a threat with any natural roll of 12+. couple with True Strike (which also adds +20 to any critical roll), you're almost guaranteed to turning that sneak attack into a critical. Get Weapon Finesse and Cat's Grace too!
3 - Also, try and avoid combat spells that can't be used for sneak attacks. Give preference to spells such as Chill Touch, Shocking Grasp, Melf's Acid Arrow, Flame Arrow (as opposed to Fireball). Archery feats like Point Blank Shot also work with the ranged touch spells.
4 - Get some spells that incapacitate your foes in a non-permanent way, like Ray of Enfeeblement. It's a great way of getting past guards that can't even carry their armors.
5 - Ray of Frost. It's a 0-level spell, and does only 1d3 damage. But get in a sneak attack with it and you'll be doing 5d6+1d3 cold damage with a 0-level spell!
6 - Haste. It's uses are legion (escape, combat, reconaissance).
7 - Jump. +10 (IIRC) to Jump checks is a great boon!