Webmaster tools has no effect on your website, other than being able to(Not sure if they do it) find out what websites a person owns. WMT is simply a way for google to inform you about your website's status, it has no effects on your rankings whatsoever. Infact, you might even find it useful to know where your keywords rank, what keywords are gaining, which ones are dropping etc., besides the other obvious uses.
OOoohhhh noooo...... They DO use it to find out what websites a person owns.
Let me sketch a scenario:
I owned about 80 sites in a private blog network.
One of these was in my WMT with my main business site, as well as about 3 or 4 of client sites for which I built websites and that I submitted sitemaps for or checked the useful stuff like which keywords are they being found for etc.
I used BMR to build links to my main business site. Google gave me the 'unnatural links' warning in March and penalised my site to > 50 (previously being in #1 for my main kw).
That was bad enough. But about 3 weeks after that Google:
1. Deindexed all the sites in my WMT
2. Deindexed all the sites that it could find with my main email address associated with the registration (the same email address it picked out of the sites in my WMT)
You see, I was a trusty little fluffy bunny believing in the GOOD GOOGLE (or stupid Google). I believed that the Google algorithm was too stupid to read registry details, and that they would never have enough manpower to manually search for sites involved in SEO practices of the darker hat variety. Well, we have all been proven wrong. They have a whole Spam team sitting there just doing that....
So, no. Do not use WMT if you are doing ANYTHING REMOTELY not white hat (in other words, just building content for your site). If you do any link building of any variety whatsoever, then it is a bad idea to use it since you are just giving them info about YOURSELF. Not about your site, that they have already. Just out of interest sake, is anyone aware of anyone who got penalised for unnatural links but who didn't have WMT??? I am not talking about Penguin, I am talking about the period when 'unnatural link warnings went out' and a site immediately dropped > 50.