These are mostly collected for my own reference, so that I can quickly find them during my trip, but they may be of interest to readers as well. Inclusion of a site on this list (or on the linked maps) doesn't necessarily mean that I will visit it - some I'm just recording for reference, and my itinerary will be at least partly decided spur-of-the-moment. See also my earlier posting. I will probably continue updating this entry rather than writing new entries for additional links; but reports when I'm actually on my trip will go in new entries.
Google Maps: Nara (MOL 12/MCFG+2 conference venues); Osaka; Kanazawa and Hakui; Maibara; Kanda/Tokyo. One unexpected benefit of Google Maps is that I can use Street View to preview my walking routes; that's certainly not foolproof, but it means I'm less likely to get lost searching for places when I actually arrive. For instance, Kume no Heinai-dou turned out not to be where I expected based on text descriptions, and I think I saved myself a frustrating hour of searching for it in real life by locating it in Street View first.
Rail transport links: japan-guide.com's top page on Japanese rail system; Hyperdia online schedule lookup ("dia" seems to come from "daiya" which is Japanese for "railway schedule," apparently short for "daiyaguramu" even if the schedule is presented as a table of numbers instead of what "diagram" means in English); English Web sites of JR East and JR Central; JR West (JR West is Japanese-only for practical purposes; the English side of the site is pretty much useless).
Osaka Visitor's Guide links (brief descriptions of sites of interest, in English), and the sites' own Web sites (often Japanese-only): Imamiya Ebisu Jinja, which enshrines Ebisu (described in my earlier posting; its own site); Abeno Seimei Jinja, which enshrines a noted 10th-Century mystic who's been used as a character in pop culture works such as the anime Magical Shopping Arcade Abenobashi, and for whom the Abeno neighbourhood may be named (its own site); Sumiyoshi Taisha, head shrine of the Sumiyoshi network (its own site); Osaka Castle (its own site - in English); The Momofuku Ando Instant Ramen Museum (its own site); Nambayasaka Jinja, which enshrines the protective deity of the Namba neighbourhood (its own site; popular place for tourist photos); Sukunahikona Jinja, which enshrines a deity of medicine (its own site).
Ishikawa Prefecture Tourism Guide - good resource on multiple sites in the Kanazawa area. In particular (deep links into this site): Keta Taisha (shrine to god of marriage; its own site); Myouryu Ji (booby-trapped Buddhist temple; its own site); Shirayama Hime Jinja (head shrine of Mt. Haku network; its own site).