A Certain Scientific Railgun (TV)

In ep 4, when the lady finally found her car, the car she drives looks strikingly similar to a Lamborghini Gallardo.

The phone Ruiko uses is similar to an iPhone with an sliding unlock screen as seen in near the end of the ending theme. Owners of the phone order from left to right: Mikoto, Kuroko, Ruiko, Kazari. You can see them holding their phones in the very beginning of ep 4.

The Opening Credits lap over onto the Opening Credits of To Aru Majutsu no Index. The scene where Mikoto is drinking juice, and Kuroko teleports onto her is in both Index and Railgun, but shown from different angles.

Uiharu and Saten can both be seen in OP1 and OP2 of Toaru Majutsu no Index

The sequence of Episode 13 on the moon between 13:15 and 13:54 is a tribute to the 1968 film "2001: A Space Odyssey", featuring the iconic black monolith, Richard Strauss' "Also sprach Zarathustra" and Shirai briefly wields a femur as the ape did in the opening of the film.

In the 2nd opening sequence (starting at ep 15), between the scene with Uiharu doing push-ups and Kongou walking with her 2 friends is split-second shot of Touma being chased by Index in the foreground.

In the 1st special an Alastor Shakugan no Shana's necklace is being sold with the crepes.

When the teacher is explaining personal reality and asks Saten, he gives the example of Schroedinger's cat and locks Sphinx in. When he opens the box again, Sphinx has been replaced with a white version of the mini tiger from Toradora. 

The four girls sitting at the table at Josephs in ep 12 are members of ITEM, a group which is featured in the Toaru Kagaku no Railgun Manga.

The rifle that the Anti-Skill members use is the SIG SG 552.

In the first episode of the MMO special (Much More Railgun), Yomikawa Aiho mentions all the things she likes that sound like "jean". One of those things is a child inventor called Jean which is a reference to the anime character with the same name from "Nadia: The Secret of Blue Water".

In the second episode of the MMO special (Much More Railgun), Uihara talks about a yellow mouse that is no longer cute when you evolve it. This a reference to Pokémon's Pikachu.

In episode 1, at around 14:33 you can see characters resembling Shana and Kazumi Yoshida, from Shakugan no Shana, waiting in line for crepes.

In episode 1, at around 15:17 you can characters that resemble Taiga Aisaka, Ryūji Takasu, and Yasuko Takasu from Toradora!.

In episode 4, at 03:55, Misaka puts down a magazine with two girls that resemble Shana and Chigusa from Shakugan no Shana on the cover.

Not only do the people on the cover of the magazine in episode 4 resemble characters from Shakugan no Shana, the magazine's main feature IS Shakugan no Shana, as it displayed on the front. In fact, all the of the magazines in that store had relevance to real-world material (as well as were magazines eerily similar to those you can find in a conbini in Japan).

In episode 07 when Uiharu and Shirai are looking over the computer, at 05:32 it shows a monitor, underneath the windows is "OOG" in red, yellow, and blue, resembling the OOG in the popular search engine "Google"s logo.

In episode 17 characters from the previous series Toaru Majutsu no Index make cameos chasing a dounut filled trash can and at a fast food resturant.

In Episode 18, Misaka and Shirai are spying on the lady Dorm Supervisor buying pizzas from "Pizza Hut"

In episode 20 when Misaka was admiring the Gekota mask at the festival, the mask on the right of the one directly below the Gekota mask resembles Taiga Aisaka from Toradora.

In Episode 21 around 13:45, you can slightly hear a radion communication.The use language is english in place full of japaneses speaker.