If there's one thing I found troublesome about XBMC, it's the poor support for anime shows out of box. I get that anime are done a little differently and that there's a separate scraper for anime information, but even that is a tad out of date.
The majority of the shows I had weren't scraped. Either due to different naming conventions or they just weren't matched at all.
Filenames
First of all, unlike TV shows, anime is treated like one big season. Your episodes should follow the naming convention of "Show Name - ep001.mkv". The important bit is "ep123" which lets XBMC know the episodic order.
Specifying source for metadata
In comes "AniDB.net Scraper Mods for Anime TV shows and Movies" by scudlee, which is a well maintained scraper primarily for anime. There are also a bunch of improvements to help with matching the titles to the right show.
The naming of this mod could have been a bit better, but it gets the job done well.
If your show still doesn't appear, you can tell it to scrape from a specific URL on aniDB.net by creating a file called "tvshow.nfo" in the show folder and pasting a link to the information.
For example Gintama (season 1), Gintama` (season 2) and Gintama Enchousen (season 3) are an absolute bitch to get right. Have no fear, just put the episodes into the right folders and place "tvshow.nfo" in each one.
For each file, paste in the direct link to each show accordingly and it'll scan right into XBMC fine. You may have to remove the show first in order for it to re-scan.
So in "Gintama\tvshow.nfo" (Season 1):
http://anidb.net/perl-bin/animedb.pl?show=anime&aid=3468
For "Gintama`\tvshow.nfo" (Season 2):
http://anidb.net/perl-bin/animedb.pl?show=anime&aid=8126
And lastly, "Gintama` Enchousen\tvshow.nfo" (Season 3) I have:
http://anidb.net/perl-bin/animedb.pl?show=anime&aid=9427
If you want to customise the Season 3 name a little, you can do this.
<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<tvshow>
<title>Gintama` Rush</title>
</tvshow>
http://anidb.net/perl-bin/animedb.pl?show=anime&aid=9427
This way you can customise the name but specify the URL to fetch information from.
This is the only way to truly enjoy Gintama and the pure Jet Armstrong Cannon insanity that comes with it!