Aside from familiar synergies and sneak attacks, a great way to make your rogue/mage more effective is by using spells to boost the rogue's many skills. Here are a few ideas.
Hiding: Under the 3.5 Dungeons and Dragons rules, you can only hide if you have concealment or cover. Fortunately, several spells can help with that. Obscuring Mist, Fog Cloud, Darkness, and Blur provide concealment -- though your DM might balk at letting you hide in the concealment of a Blur spell!) Most DMs would allow illusions from Silent Image on up to provide concealment as well, if you are clever with how you use the spell. And of course, Invisibility offers total concealment and great Hide bonuses: +20 if you are moving, and +40 if you are standing still, per the SRD. The Shrink Item spell is handy to "create" a big object to hide behind. And to let you talk with the rest of the party while sneaking around without revealing your position, the Message spell is one of the best cantrips available. (In fact, in earlier versions of the game, Message was a first-level spell.)
Hiding, Moving, Balancing, etc: Certain skills include a penalty if you use them while moving at normally. You can move at your normal speed while hiding at a -5; if you move half your speed there is no penalty. The Expeditious Retreat spell effectively doubles a human's speed to 60, so your new "half speed" is normal speed for the rest of the party.
Escape Artist: You can cast Grease on your armor or clothes to give you a +10 bonus on Escape Artist checks.
Disguise: From Disguise Self to Alter Self, Poly Self, and on up, these spells grant a +10 bonus on Disguise checks.
Use Rope and Climb: Animate Rope offers a +2 on Use Rope checks. A rope used for a Rope Trick spell is easy to climb (DC5). Spider Climb may make these bonuses moot, of course.
Sleight of Hand: Although no spell specifically gives a benefit to pick pocket attempts, use Detect Magic and Arcane Sight to select the best objects to lift. Shrink Item is a good spell when you want to spirit away bulky objects.
Boosting skills in general: The second-level buff spells -- Cat's Grace, Eagle's Splendor, etc -- grant a +2 bonus to skill checks based on the boosted stat. The short duration makes them less useful. Heroism is a fantastic buff spell -- +2 on attacks, saves, and skill checks, for a longish duration! The Alter Self spell grants the racial skill bonuses of the assumed form, so for some skills that's a boost.
And let me add a few thoughts on making good use of your wizard/rogue. Since you have the Scribe Scroll feat, stock up on scrolls for all these spells -- many of them are useful only some of the time, and you don't want to clutter up your head preparing them. Instead, if they are available as scrolls, you'll be able to cast at will. Keep spells in your head that you know you will cast, like mage armor, or that you can cast on an enemy, like Glitterdust, since the save DC for scrolls is almost always lower than for spells you cast from your head.
Finally, if you are considering the Arcane Trickster prestige class (and you should -- it is designed for the arcane rogue), then make sure you pick up the required skills and the Mage Hand spell.
