The symbol for the Mori observation deck is "discounted admission", though it doesn't say how much, and the one for the aquarium you mentioned is "park entry", so I guess it's free admission, but perhaps there are other things within that you might have to pay for?

The fifth museum down, which I will write as Shi-ta-machi to avoid the automatic censor (it's the Shi-ta-machi Fuzoku Shiryokan in Japanese), is quite interesting, and I like the Crafts Gallery at the Modern Art Museum (guess that depends on your feelings re: crafts). I've heard good things about the Tama Zoo, although it's a bit distant.