World of goo: http://www.worldofgoo.com/
is fun but it might be a little to complex for a 3 year old.
and also there a bunch of I Spy, hidden object find-them games from Big Fish: Play Hidden Object Games > Download Games | Big Fish
But do you take away the mini-figures in real life? Because little kids smacking around the mini-figures isn’t super different from virtual mini-figures smacking each other around.
I played Sushi Cat once a few years back. Because of that, we always say that one of our cats, who could always eat, is trying to “achieve full belly”.
Depending on age, it may be too sophisticated for kids to get through, but: at one part you melt a dude’s face off. A friend gets killed (off camera I think), and you see his (VGA graphics) mangled corpse. Monkey Island and the like have parts too, although it’s the (intentionally and humorously) most tame depiction of pirates anywhere. It was part of my upbringing and ever kid should play it at some point.
Scribblenauts mostly requires the user to have the capacity to think of violent things, so I doubt they will accidentally conjure an “evil gigantic ghostly zombie shoggoth.” Some of the quests, depending on game version, might be a bit violent.
(Going for good, “cute” games): The Amanita games (Machinarium and Botanicula), along with their other games e.g. Samorost, aren’t bad that I remember. Reus does have tiny people warfare and might be a bit older in terms of gameplay. Solar 2 maybe if sentient celestial bodies are ok.
Puddle comes to mind, immediately. It even has a level editor.
Hopefully “blobs of goo evaporating” isn’t too violent.