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Could it have been Putt-Putt Goes to the Moon? It had a lot of stuff that sounds similar.
Necro-ing this because I realized that the first one was some iteration of Math Blasters. I probably misremembered the details, but I did an image search and found screenshots that were definitely the game I had in mind.
Still not sure about the second one,. The name of the series mentioned in the previous post sounds really familiar, but it might not be the one I had in mind. I'll try looking it up, though.
edit: OK, it was the second one that was Thinkin' Things. Looks like there were several, but the Wikipedia article does mention the critter-based spinoff I remembered, so I know it's the right series.
Thrasher, I doubt you'll see this, since your reply is over three years old by now, but thanks anyway!
Edited by SapphireBlue

I've got two games that I'm curious about. Both are PC edutainment games, probably from the mid-to-late 90s.
The first was one of those games where you had a central area, and could access a number of minigames from there. It had a space theme, and the central area was a spaceship. There was one minigame where you were on this planet with a lot of craters, and you were playing a kind of "whack-a-mole" thing. These weird, brightly colored, cartoony-looking aliens would stick their heads out of the craters, and you'd hit them with something. I don't remember if you had a bludgeon or if you were shooting something at them. I can't seem to remember any of the other minigames, or what exactly the goal of the game was. I think there must've been more than one of these games, because I remember a friend having one that looked similar, but had different minigames.
The other one is similarly hard to remember, and again, all I have is bits and pieces. It had the same kind of "central area" format as the other one, but that's the only thing they had in common. This central area was mostly dark, I think, with spotlights on the things you could do. I know there was at least one minigame that involved music, but I don't remember anything about it besides that. The thing I remember most clearly was some weird little game where you were making these fluffy critters. I think they were fluffy, anyway. You were in a building, and people would come to the door and ask you to make them one. They'd tell you the specifics, and you'd give it to them. I remember that those things eventually got their own spinoff - something to do with a town full of them. Aside from that, I remember there being more than one of these games, but I only ever played this one because I was too young for the others.
Come to think of it, the one with the music minigame and the one with the critters may have been two different games, but I'm not sure.
I know this isn't much help. I'm not too concerned about finding out what these were, but if anyone knows what I'm talking about, I'd appreciate it.
Edited by SapphireBlue