Due to no attack roll IMO just one trip.
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Nothing in Toppling spell states anything about attack rolls:
for reference
Toppling Spell (Metamagic)
Your spells with the force descriptor knock the affected creatures prone.
Benefit: The impact of your force spell is strong enough to knock the target prone. If the target takes damage, fails its saving throw, or is moved by your force spell, make a trip check against the target, using your caster level plus your casting ability score bonus (Wisdom for clerics, Intelligence for wizards, and so on). This does not provoke an attack of opportunity. If the check fails, the target cannot attempt to trip you or the force effect in response.
A toppling spell only affects spells with the force descriptor. A toppling spell uses up a spell slot one level higher than the spell's actual level.
It seems to trigger once if damage is dealt by a spell, not once for each time the spell deals damage. So I would rule you get one trip attempt.
I'd say that if you target the same target with multiple missles, you only get one attempt on that target, but if you target multiple targets, each one has the chance to be tripped. Since the metamagic states 'if the target takes damage...' and since with magic missle you can choose multiple targets, if they're damaged there's a trip attempt.
Sneak attack effects only get added once so I would imagine the same logic applies.
one spell, one trip. there's precedent that if you hit different targets you can only choose to affect one of them with additional effects (sneak attack and scorching ray).