In Japan, there are quite a few mangaka (manga artists) who are video game fans, and sometimes, references to their favorite games wind up in their works. Please note that only professionally published manga is covered here; for obvious reasons, doujinshi ("fan comics") are excluded.
Cactuars in Love Hina
This is an odd one. Aside from their appearances in multiple Final Fantasy games, Cactuars actually make minor (very minor) cameos in the Love Hina manga by Ken Akamatsu. (eg: Sarah throws a large stone Cactuar at Keitaro, hitting him in the head.) If anybody knows of any other manga that Cactuars appear in, please let us know.
Tifa, Vincent, and Yuffie cosplayers in Faeries' Landing
In the first volume of You Hyun's manhwa (Korean manga) Faeries' Landing, several of the chapter intro pages show the characters Fanta and Ryang dressed in FFVII costumes. We don't know if there are similar pages in later volumes, but it's very likely!
Here are a couple of images from Faeries' Landing that contain FFVII references:
Tifa and Yuffie cosplayers in Genshiken
In this manga, which follows the members of an "otaku club", there's a cosplayer character named Kanako Ohno. Among the characters she cosplays as is FFVII's own Tifa, while an American character named Angela cosplays Yuffie.
Images of these cosplays and others are available at this Genshiken fansite.
Cloud, Tifa, Vincent, Cait Sith, and Red XIII in Descendants of Darkness
Also known to its fans as Yami no Matsuei, this manga features five FFVII characters in the background of a panel in Vol. 3. Here's the panel from the official English version:
Also, in Vol. 4 of this manga, there's a brief appearance by a fortune-telling cat named Cait Sith (translated in the official English version as "Ketto-C"), which the author claims is "not just a rip-off from that video game! The name comes from a Northern European fairy spirit or something (Irish, actually. See the Name Origins page for details --Reeve). (Ha!) Both characters were just inspired by the same creature, but if you want to think I copied it, I can't stop you."
Compiled July 2005. Last updated February 2007. Thanks to our cameo spotters: ChibiTaryn, Mogfreak, Akkun, and Freya.