I'm actually emailing my IP law professor right now to ask him about some of the intricacies of these situations.  Especially when it comes to high schools using the logos (http://home.mchsi.com/~b.blewett/Conferences/BigSiouxConference.htm#TriValley)

in terms of logo copyrights, but I do know of an instance where color did not matter.  My high school in Tulsa uses the University of Miami broken U as its primary emblem, and due to my school's notoriety in the state as the elite sports high school, it was only a matter of time that Miami caught wind of it.  Rather than sue the school, Miami reached an agreement to have my school pay an annual fee to use the logo, a meaningless 1,000 a year if I'm not mistaken.  Because the figure is so low, it looks more like Miami was pushed to make a deal for deals sake more than a worry over copyright enfringement.  

First of all... they're probably Trademarked, and not copyrighted.  A modest difference to the layman, but a substantial legal difference.  First trademarks last into perpetuity, while a copyright lasts 95 years past the life of the author (the 95 year extension is known as the sonny bono amendment).  Second the purpose of a copyright is to protect the artists investment in creating the work (like a cd, movie, etc...) while the main purpose of a TM is to identify the source of a good.  TMs are also indicated by a (R), the only difference being one is a federally registered TM, and the other is not.

Second, with the high school teams, there may be a licensing agreement in place (like what ohnokoolaid described).  BUT in generally in order for there to be trademark infringement there must be a risk of confusion to the consumer... I doubt very highly that someone would confuse the Tri-Valley Mustangs with the Denver F***ing Broncos.  An aside about college... There is a well publicized fight between Wisconsin and any highschool who dare use their "motion W" design.  So colleges can and do enforce their trademarks against high schools, but generally it looks like pro teams can't/don't/ or are licensors.

Finally with regard to the German pro team that started this whole post... They've obviously modified the logo by changing the color, but that's probably (definately) not enough to avoid infringement.  Further the fact that that team is professional AND the Broncos logo has a preseance in Europe and Germany (logo's on the players jerseys in NFL Europe), the likely legal answer is that there must be some sort of licensing agreement in place or the Germans are asking for WWIII AGAIN.

There is one more possibility that I can think of, though I think it HIGHLY unlikely.  Germany and USA are both signatories of severaly international copyright and trademark treaties, the gist of which are a trademark in one country is as good as a trademark in another so long as a few hoops are jumped through.  IF the Broncos never applied for their international TM, then it would be unenforceable in Germany, and the Stallions in question would essentially be able to do most anything they wanted with the logo (in Germany).

I hope most of this is right... I am not a Lawyer, but I am a law student, currently in an IP class.