The analysis is based on the reaction times (and, secondarily, the error rates) for the various conditions for which the words (or the pseudowords) differ. A very common effect is that of frequency: words that are more frequent are recognized faster. In a cleverly designed experiment, one can draw theoretical inferences from differences like this. For instance, we might conclude that common words have a stronger mental representation than uncommon words.
Lexical decision tasks are often combined with other experimental techniques, such as priming, in which the subject is 'primed' with a certain stimulus before the actual lexical decision task has to be performed. In this way, it has been shown that subjects are faster to respond to words when they are first shown a semantically related prime: participants are faster to confirm "nurse" as a word when it is preceded by "doctor" than when it is preceded by "butter".
Meyer, D. E., and Schvaneveldt, R. W. (1971). Facilitation in recognizing pairs of words: Evidence of a dependence between retrieval operations. Journal of Experimental Psychology, 90, 227-234.