I use a Academic Writing Check for most of my academic writing, including my thesis. It checks for:
- passive voice: don't use the passive voice if you can help it.
- duplicate words ("the the"): this has saved me many times.
- wrong abbreviations: for example, i.e (no second period)
- bad typography
- and some others
To check missing or duplicate labels, I use pdflatex (with this very cool Makefile). It prints a warning message anytime some of the above occur.
I'm not sure how you would check for wrong citations, but pdflatex will tell you about undefined references. For certain words you don't ever want to occur, just use grep.
The last check I do is for overfull hboxes, you can visualize them in your document by setting this in your preamble:
I found that on the LaTeX stack exchange, you will no doubt find the answers there a great resource as your write your document. Good luck!