Detective Conan

Detective Conan, an anime about a teenage detective shrunk into a little boy.

Bakemonogatari
Ran from 2009-12

Gintama
In episode 8 Gintoki does a spoof of the regular 'shoot Kogoro and do a deduction' scene.

Hayate no Gotoku
Conan appears in ch. 30 of the manga (in fact that whole chapter was done in the style of a Detective Conan mystery).

InuYasha
Ran and Shinichi might have been at the school festival in ep 128.

Conan might have been shown reading an IY manga around same time.

Yakitate Japan
Ran from 2004-6 In one episode the character Pierrot transforms into Conan

=Cameos=

Magic Kaito
Most of the Magic Kaito characters have appeared in Detective Conan, the most famous of all being the Kaito Kid. This is specifically because Magic Kaito was made before Detective Conan (they're by the same author) but failed to be popular.

Yaiba
Another series by the same author. Magic Kaito, Detective Conan and Yaiba all meet in the second series' first OVA, as well as having Cucumber Man exist as a cell phone strap.