For gear, make sure to consider the mundane gear. At low levels (the places where folks like Rogues actually can do B&E well) mundane gear is what matters. Shadowsilk Armor, the Muffling enhancement for armor, Silent Shoes, Earthsilk Rope, and a variety of other items are very useful. Another amazing piece of gear, though it's magical, is the Shadow Hands from Tome of Battle. Shadow Jaunt is VERY handy.
I'd of course put Factotums well above Rogues in this. Int to all Dex and Str based skills blows Skill Mastery out of the water at the levels where you actually have Skill Mastery, and +level to any skill is extreamly potent. Plus, the ability to actually cast Knock and thus get through Arcane Lock is critically important. Permanent AMFs are insanely hard to put up. Arcane Locked Doors, however, stop Rogues cold unless they have Knock, and unlike a Factotum, a Rogue can't make a wand of Knock so they have to purchase one (and hope it's available to purchase). Remember also that a Silence spell with an adamantium weapon can just cut through most barriers... the door may be magically secured, but the wall next to it probably isn't. And they can cast Alter Self (into a Skulk or Whispergnome) for extra fun.
Beguilers are also much better infiltrators. They lose things that don't matter much to infiltration (like Sneak Attack) but are Int based (more skills in the long run) and can cast Knock as well as use illusion magic to sneak in much easier.
And don't forget Swordsages. The Mountain Hammer line of strikes takes out any physical obstacle while the combination of Shadow Jaunt and Cloak of Deception gets them anywhere. By about level 5 they should have little trouble getting anywhere. Eventually they'll get the ability to phase through walls. Or you can take a level of Swordsage as a dip at level 5 and just get those utility manuevers added in to any other class. I'm a big fan of Factotum X/Swordsage 1 as an infiltrator... the throw manuevers are hilarious with the Factotum 3 ability, after all.
JaronK