So technically my mother language is Japanese. Later, when I was 7/8 years old, I moved back to my home country and quickly grasped the new language. Now, all I know is this language and English. I literally forgot most of Japanese and have difficulty conversing in it. I can still read Japanese characters and recognize some words though, and I’m sure if I take some classes, I can quickly relearn everything. But I don’t speak it on a daily basis anymore.
The problem is I really don’t consider I’m good at Japanese right now, but it is my first language (there is a checkbox for first language in common app). So should I list it or not?
By the way, the language I’m most proficient in right now is that of my home country.
No. If you can’t carry on a conversation in Japanese on any subject that you would be able to converse in English, then you’re not proficient.
Common App Help Center says: “Proficiency in a language is about how comfortable you are using another language as a form of communication. In order to be proficient, you must be able to communicate effectively and converse comfortably.”
To me, that doesn’t mean you have to be able to talk about absolutely everything you can talk about in your main language – debate politics, analyze literature, make pop culture jokes, etc – because that’s fluency or near-fluency. But it also doesn’t mean just a few stock phrases.
I think students are often advised to list languages studied in school on the Common App. So, if you’re using “typical high-school language student” as a benchmark for what Common App means by “proficient,” what level is that, exactly? Well, the U of Oregon did a study to find out how proficient high-school students typically become in language studies; by four years, they were generally at Novice High or Intermediate Low on ACTFL levels. If you’re curious what that means, here are the ACTLF guidelines:
http://www.actfl.org/publications/guidelines-and-manuals/actfl-proficiency-guidelines-2012/english/speaking
And here’s another, simpler benchmark: Imagine that you’ve applied to a school that requires an interview. You get interviewed by someone who, it just so happens, speaks the language you’ve listed for “proficiency.” And they decide to chat with you a bit in that language! OK, now what happens? 
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Not to be critical, but you may want to spiff up your English writing skills. I had trouble following your description. What is your home country’s language?