I have a lexer built that streams out tokens from in input but I'm not sure how to build the next step in the process - the parse tree. Does anybody have any good resources or examples on how to accomplish this?
I would really recommend http://www.antlr.org/ and of course the classic Dragon Compilers book.
For an easy language like JavaScript it's not hard to hand roll a recursive descent parser, but it's almost always easier to use a tool like yacc or antlr.
I think to step back to the basics of your question, you really want to study up on BNF-esque grammar syntax and pick a syntax for your target. If you have that, the parse tree should sort of fall out, being the 'instance' manifestation of that grammar.
Also, don't try to turn the creation of your parse tree into your final solution (like generating code, or what-not). It might seem do-able and more effecient; but invariably there will come a time when you'll really wish you had that parse tree 'as is' laying around.