I think it comes down to putting all of your eggs into a single, unnecessary basket. Rank checking software is dirt cheap, heck, there are even free
solutions. My recommendation is that for rank tracking, use paid services
like Serpfox, or RavenTools.
Most of us have been burned by the big G at one point or another. Its the
same reason you see sites completely deindexed all at the same time, or
when one sites banned in Adsense, so is the whole account.
For most of us, Webmaster Tools is completely unnecessary.
The reason I use Webmaster Tools and recommend it more over any other tool, is because you can find keywords you didn't even realize you were ranking for, and improve on those. If you are ranked #19 for a keyword and getting lots of impressions but no clicks, then with a bit of work, you could bump that up and start seeing some clicks.
People are always obsessed about ranking for a certain set of keywords, without really checking what they are naturally ranking for. They are fighting against Google, instead of working with them.
I use other rank trackers to check my DAILY updates, but every Sunday I check Google Webmaster tools to see whats going on. Again, my opinion is that if Google wants to find all your sites, they can do it fairly easily, because most people host all their sites on the same ip and by checking the whois info, registration dates etc, it becomes quite obvious who owns what sites.
I also would think Google knows that SEO companies track the rankings for multiple sites that dont belong to them, and so even though they may be doing blackhat on 1 site, doesn't mean they are doing it on all of them.
If someone else can provide me a ranking service that shows every search term that gives me impressions, for free preferably, we can talk. Until then, Webmaster Tools is my recommendation.
