I have played a number of Factota over the years at varying levels with with different degrees of multiclassing... and in my experience they are rather lacking as a primary class. They have a variety of supporting abilities that give fantastic boosts, but they lack a primary focus. Let's check out their major abilities:
-Trapfinding: At least you're more useful than the rogue.
-Cunning Insight: Great way to ensure an attack lands or deal lethal damage, particularly at low levels. Can debatably work with ability damage, which can potentially be devastating.
-Cunning Knowledge: Grants a 1/day modest boost to an attack with Iaijutsu Focus. Really shines on niche skills that you'd only use 1/day anyway, like Forgery, Decipher Script, Appraise, etc.
-Arcane Dilettante: By picking versatile spells, they can potentially have a trick up their sleeve to get out of a tight situation. Early on this ability is pretty lame, limited to Prestidigitation or Ray of Enfeeblement or Nerveskitter. Later on Alter Self and Polymorph can give them a significant combat boost for one combat. Vampiric Touch and Shivering Touch combo with Cunning Insight, even if it doesn't apply to ability damage. Also qualifies the Factotum for metamagic feats... which are of limited use to him beyond Extend due to his normally limited casting.
-Brains over Brawn: I find that this is the ability that sees the most use. First of all, INT to initiative is awesome. Second, picking up a guisarme enables tripping as a fairly reliable debuff, and, if the game sticks to low enough levels, then Improved Trip is very strong. It also provides a significant boost to many skills, like Tumble, and many of the movement-based skill checks that you probably don't want to fail at low levels, like Climb, Jump, and Swim.
-Cunning Dodge: In my experience this ability doesn't come up too often, but does provide you a bit of a crutch if you get caught out of position.
-Cunning Strike: Great to get some extra oomph. Works well with weapon-like spells.
-Opportunistic Piety: The healing is better than the turning. Gets you some extra staying power but is nothing special.
-Cunning Surge: This ability would be great if the class had a way to capitalize on it more. By itself, wand use and Manyshot are the only real ways to get decent mileage out of it, although it can buy you an extra move if you need it.
-Cunning Breach: This ability would be awesome at higher levels, except that, again, you don't really have a way to capitalize on it. Your attacks tend to be less than stellar, and you don't really have enough spells for all-day use.
-Cunning Dodge: I feel that if this ability comes up, you are doing it wrong. However, it is a nice safety net to have.
-Improved Cunning Defense: Definitely an improvement over Cunning Defense, but nothing special at this point.
-Cunning Brilliance: Debatably can nab you spellcasting of a 15th level wiz/cleric, but that seems lame to me. Grabbing maneuvers and a recovery method to turn into an impromptu Swordsage has been effective for me. The Warblade's INT-synergy abilities are fairly cute too. Comes way too late in the class IMO.
So we have a bunch of bail-out abilities and stuff that gives some minor boosts. In my opinion, the best abilities come at or before level 3.
At E6 levels, I have found a trip-based Factotum to be an acceptable beatstick that can also handle out-of-combat utility, with good initiative and STR checks for keeping enemies under control and Alter Self as a self buff for combat abilities.
At higher levels, though, I have found the factotum to be extremely lacking, particularly in combat.
However, I have found that Factotum really shines as a support class, particularly in gestalt. Other classes, like Wizard, Archivist, Psion and Warblade, can benefit greatly from the INT-synergy that Factotum offers... particularly the initiative boost from Brains over Brawn. Casters, of course, need to be wary of caster level loss outside of gestalt. Cunning Surge suddenly gets a huge jump in power when you have a use for your extra standard actions, like spells or maneuvers. Cunning Breach also becomes much more useful, allowing you to blow past high-SR creatures with ease, or high-DR creatures if you are going the TWF/Tiger Claw route with Warblade. Incarnate and Totemist are also very powerful with Factotum in gestalt, enabling you to be prepared for any situation without preparation. Dissolving Spittle and Manticore Belt are particularly useful with Cunning Surge.
I should also mention that Factotum works exceedingly well in Epic, particularly with gestalt, and particularly if you play with the Dicefreaks rules. Cunning Breach is invaluable, allowing you to blow past the absurd SR and DR that some creatures possess, reenabling the use of SR: Yes spells.
I find that Factotum is an excellent lead-in to Chameleon, and that Cunning Surge helps you make use of the gobs of spells you get from Double Aptitude. Factotum 11/Chameleon 9 is an excellent build for most campaigns. I find it most effective to go Factotum 5/Chameleon 2/Factotum +3/Chameleon +7/Factotum +3. The bonus feat can be used for Extra Spell on off-days to pick up more spells for the spellbook, and to share with the party Wizard/Archivist. It's lacking a bit in campaigns of incredibly high optimization, though,without abusing Extra Slot for 9ths. I find the build is strongest at 15th, when you pick up Cunning Surge and Double Aptitude. You're behind a CL and 2 spell levels on a wizard, but have the versatility of multiple spell lists and lower-than-normal-level spells, such as those from the Trapsmith or Paladin lists. I find that you're best off trying to function as a rogueish gish, that has utility spells so that the primary spellcasters can focus on their duties. You can also debatably make use of the Artifact spells from Secrets of Xendrik, which are an exceedingly powerful tool.
In conclusion (and the TL;DR i guess):
I find Factota most useful at low levels or in gestalt. I find the best ability for the single-classed factotum to be Brains over Brawn and that Cunning Surge is only really useful with another class. I find them to be a huge improvement on the Rogue, and can be better than a Fighter, and can play competently alongside Tier 1/2 classes at low levels, but are lacking in potency at higher levels. In my experience, Factotum/Chameleon is a very good combination that works well in most campaigns. Of course they pale in comparison to a well-built and well-played Wizard, Cleric, Druid, or Artificer, but what doesn't?