Thought about it for a bit, and WOW, good movies with bad special effects are surprisingly hard to come by these days, probably because:
a) "Special Effects Based" Movies either invest lots of money into CGI and/or have bad storys anyways
b) ESPECIALLY 2009 showed with District 9 and Moon that you can create good special effects even on a "low" budget these days.
c) If a movie does not focus on special effects, chances are you won't even notice
That said, if it's recent enough, Donnie Darko had pretty bad computer effects and a very good story.
V for Vendetta has a kinda good story if you don't know the original graphic novel, and doesn't really shine with good effects, however, one of many occasions where i would argue that it's definitely "good enough".
And while i wouldn't say for myself that these movies had good stories, some people liked the plots of "I Am Legend" (what a piece of shit) and the Ang Lee Version of "Hulk" (bored and confused), both of wich had pretty bad effects.