DiG Japan
https://digjapan.travel/en/basic/
JNTO Japan Weather Forecast for Traveler
https://www.jnto.go.jp/weather/eng/index.php
Navitime
(Other than the connection info, Travel Tips tells you how to get cash, Wi-Fi, rechargeable IC cards for transportation and shopping, what to pack, etc.)
https://japantravel.navitime.com/en/area/jp/route/
Japan Transit Planner (Mostly train connection)
*Note: You can depend on Google Maps, too, especially for walking and taxi options!
https://world.jorudan.co.jp/mln/en/?sub_lang=nosub
JAPAN Welcome Guide for Muslim Visitors (JNTO)
https://muslimguide.jnto.go.jp/eng/
Japan Masjid Finder
https://www.masjid-finder.jp
Yelp, Lonely Planet and other English travel sites also list user recommendations on Japanese restaurants.
Tabelog
A Japanese version of Yelp on Restaurants, with more listing than Gurunavi, mostly recommendations from guests. Click ‘my location (現在地) ’and then type in the food you want.
https://tabelog.com/en/
Gurunavi
A Japanese version of Yelp on Restaurants, whose language options and interface are user friendlier than Tabelog. More precise restaurant information from the proprietors themselves.
https://gurunavi.com
Food Diversity Today
https://fooddiversity.today/en
Halal Gourmet Japan
https://www.halalgourmet.jp
Japan Guide
(Tourism information. Its user forum is a helpful place to get answers to your questions.)
https://www.japan-guide.com
Japan National Tourism Organization (JNTO)
https://www.japan.travel/en/
Tax exemption info
https://tax-freeshop.jnto.go.jp/eng/shopping-guide.php
Lonely Planet
(Recommendations from people sharing your culture may resonate with you better.)
https://www.lonelyplanet.com/japan
Japan Info(Interesting articles on culture, life and travel in Japan.)
https://jpninfo.com
Japan Monthly Web Magazine
(by Japan National Tourism Organization. Not the timeliest, but with deeper insights and quality reading on various topics)
https://japan-magazine.jnto.go.jp/en/