Toto recorded a song called "99," but apparently the band intended it to be taken not as a paean to Barbara Feldon but instead as a "mock-Orwellian cautionary tale" about the future, a future in which "depersonalized people have numbers, rather than names," according to Alert Reader Will G., who also notes that Toto is dumb.
The all-female ska band Agent 99 used to be pretty famous in ska circles, evidently. They broke up a few years ago.
Also, there was an obscure early-'80s rockabilly/punk/power-pop (?) group called "Get Smart," but I don't think that's a TV reference.