For my SHS1 Oral Communication classes, I wanted to know which of the most useful words in English may or may not have been covered by students during their junior high EFL classes. To do this I compared, on the one hand, a vocabulary list I made out of all the Ministry approved JHS textbooks and, on the other, the GSL's list of the top 1500 high-frequency words, and then found out which words were common to both lists. Finally, after lopping off grammar (function) words such as "a. in, about, however", adding a simple Japanese gloss and including each word's GSL's frequency rating if available (if not, the word was marked "JHS only"), I came up with a list of 1000 or so words I could work from when creating teaching materials.
Note that the file is large (300Kb) and opens up on a separate browser-page (rather than in the frame). And please, if you decide to use it, do let me know -- it's always nice to hear I'm not alone in Japanese secondary-school land. Anyway, here's the list.
For info about vocabulary learning software, here is a very worthwhile article by Michael Geffon.