Yup, I found out about this topmoxie crap when I installed 2.1.3
The only reference I found is at the very end of the license agreement. I'm almost certain that I checked this and found no reference, but I since deleted that file. The new download of 2.1.3 does have the reference, so I either did not see it (doubtfull in my mind, since I was going through different versions at the time looking for the newest one without topmoxie), or they forgot to include this in the agreement and updated it.

At any rate, I now use FreeWire, which does not have this crap. Like the other person says, I understand the need for revenue, but they are well aware that nobody really reads those agreements anyway, so putting it there, and only there was a dirty trick in my book. They can always say "hey, it's in the agreement", but I am a software developer, and quite computer savy, and it got me too. I have of course deleted this from my system, along with 2.1.3.

Note that the agreement for 2.1.1 makes no reference to topmoxie, so I would hope this one is safe. you can get it from LimeWire's site here:
http://www3.limewire.com/download/
As far as cydoor goes, it is supposedly uninstallable.

For those who want a much more friendly version, you can get FreeWire here:
http://www.freewirep2p.com/
It has no banners either. Or if you prefer, you may like the nicely done AquaLime, available here:
http://mamiyaotaru.mangatoanime.com/
It was done with a very attractive skin made to look like the Aqua theme available on the Mac.