Wakan is all I use, and I will (hopefully) soon be done with all jouyou kanji...
Just memorize them by radicals (e.g. remember 語 as 言 五 口 rather than as a random collection of lines), learn some of the most common compounds for each kanji (no point memorizing 季 by itself -- but 季節 is a common word), and make
sure you can actually handwrite them without looking 5 minutes later (even if you never plan to actually handwrite -- just imagine how questionable your grasp of the English alphabet would be if you needed a computer to remember how to write an 'A'... it does wonders for long term memorization, too)
(Disclaimer: there are a bunch of errors in the stroke orders given by Wakan. If in doubt, double-check with
WWWJDIC, which, as far as I know, has them 100% correct. I also kept a .txt of all the errors I noticed until I got good enough at stroke order to stop checking it most of the time, so ask me for it if you're interested)