I think that one problem with independent reading is that almost no texts take the time to inform you of their difficulty level.
When I go Chinese book shopping nowadays, I count the number of unknown words in a given page at three random parts of the book. If it's above some tolerable lookup average (say, three or four words per page, with some regularity of the missed word throughout the chapter), I shelve it and look for something easier. I give annotated books more slack, because phonetic lookups are easier.
When it comes to harder reading online, I always use a highlighting dictionary for unknown terms. But don't
use mouseover dictionaries, because they're a bigger annoyance than help. I downloaded Lingoes with the Vicon Chinese(T)-English and English-Chinese(T) dictionaries. The Vicon dictionaries, themselves, are slightly older versions of the Lingvo dictionaries, which you can see at http://www.lingvozone.com/
(For some reason, Russians are really motivated lexicographers, and most good translation dictionary resources come from them or Oxford.).
I don't use, and in fact I openly despise the CC-Edict, but it's a passable secondary source for unknown terms. http://www.trainchinese.com
is POS-tagging the CC-Edict, however, and cutting its definitions down to size, so you could use that, too. (Don't use their teaching resources, though, since they want you to pay for features that are free elsewhere.)