Are there spells or magic items that work on magical beasts that increase their size? That is, standard undomesticated, or trained magical beasts, not familiars or in any way companions (hence lacking the special ability share spells).
Ways to directly increase a magical beast's size
Needless to say, there aren't many.
An Intelligence 1 or 2 magical beast can likely be taught an uncommon trick allowing it to activate a psionic tattoo of expansion (1st-level power at manifester level 6—longer than most combat encounters last just in case but lower the price by 50 gp for each −1 caster level and corresponding −1 round duration) (Expanded Psionics Handbook 170-1) (300 gp; 0 lbs.). (An Intelligence 3 or higher magical beast can probably just be shown how to rub the illustration on what passes for its skin.)
Unlike the 1st-level Sor/Wiz spell enlarge person [trans] (PH 22-7), no restrictions exist on the target of the 1st-level pychic warrior power expansion [pychometabolism] (XPH 105-6) except that the power has an entry of Range: Personal, and, unlike potions, a creator can make psionic tattoos that contain powers with an entry of Range: Personal.
The 8th-level Clr spell abyssal frenzy [trans] (Fiendish Codex I 90-1) et al. for 1 round/level, in addition to other effects, increases by one size category an animal, humanoid, magical beast, or monstrous humanoid. The subject can't cast spells, use spell-like abilities, activate magic items, or use weapons other than its natural weapons for the spell's duration, but if that's not a problem, this seems the path of least resistance, despite the source's obscurity.
A staff of abyssal frenzy (8th-level spell at caster level 15) (90,000 gp; 4 lbs.) is expensive at 1,800 gp per charge, and, if not a cleric, even activating such a staff by employing the skill Use Magic Device may be problematic.
Some spells can cause the magical beast to assume a totally different form that may increase its size category. For example, if the magical beast can activate an item containing the 7th-level Sor/Wiz spell body of war [trans] (Spell Compendium 35) for 1 round/level the creature, among other effects, becomes size Huge. Likewise, the 2nd-level Sor/Wiz spell alter self [trans] (PH 197) for 10 min./level allows the creature, if capable of activating an item storing such an effect, to assume a form up 1 size category bigger than its original. Other form-changing magic can achieve similar results. I suspect, however, that this isn't what you're after.
Other, more convenient ways, I'm certain, exist, but these should get you started. I'm still hunting.
Ways to indirectly increase a magical beast's size involving possible shenanigans
I can't really endorse these methods: as a DM I don't like them, and as a player I'd feel wrong using them, but I put them out there as possibilities. Run them by the DM first and see what happens, doing your best to avoid injury.
The 8th-level Sor/Wiz spell polymorph any object [trans] (PH 263) could possibly change any creature's size category arbitrarily simply by specifying that, for example, the resultant creature be the same as it is now except, y'know, like, bigger.
When one can be found, a level 15 wizard typically charges 1,200 gp per casting of the spell polymorph any object according to Table 7–8: Goods and Services on Spellcasting and Services (PH 129, 132).
Using the rules for magic–psionics transparency (XPH 55-6), a creator could fashion, for example, a psionic tattoo of aspect of the wolf (1st-level spell at caster level 1) (50 gp; 0 lbs.), which for 10 min. transforms the creature into a Medium animal. Afterward, the once-magical-beast-now-animal can be subjected to all those spells that target animals like the 5th-level Sor/Wiz spell animal growth. Then the effect of the spell aspect of the wolf can either be dismissed by a magical beast smart enough or be dispelled by the magical beast (if it's able) or another creature.
See—although the topic's sometimes the subject of debate and, if not, outright argument—, usually spells only care if the creature was a valid target upon their casting. (Checking if a subject is a legal target constantly is a Magic: The Gathering rule but unmentioned in D&D 3.5e; for example, the spell charm person usually doesn't end if its subject is later also the subject of the spell aberrate that changes its type to aberration.) Thus this combination could leave still in place all of the spell effects that the now-a-magical-beast-again gained while it was an animal. This is not the kind of metarule that's usually exploited, being so shady that you'll need this flashlight to pull it off. Also, it's dangerous to go alone; take this helmet in case books fly at your head. And good luck.
Just to be clear, in the first case, this DM usually just straight-up bans the spell polymorph any object, finding contemplating the long-term campaign effects of the spell (like its friend the spell fabricate) impossible and its cost less than—and its functionality often surpassing that of—even a carefully-worded wish spell… with the added bonus of, for example, engaging in debates over the kingdom classification of an air elemental. No, thanks. May your DM be braver and more patient than this one.
This DM has fewer problems with the second option: it's enormously complicated for a relatively small payoff, so he'd probably allow it, but he'd look askance at the players were they to try identical shenanigans with much more powerful results (additional examples left to the imagination).
As far as I know, there's no canonical "Enlarge Monster". However Charm Person/Monster/Mass has a level progression of Wiz 1/4/8 so you could use that as a guideline and compare it to other spells with similar effects to ensure the level isn't too low.
Just remember if you homebrew something for the villain the players are going to want to know why they can't access it too.