Are there any particular incidents which are responsible for the low reputation Microsoft (and Bill Gates) has in the eyes of the open source community? Microsoft is clearly not the only proprietary company. Companies like Apple have done a lot worse when it comes to restrictions on software. Why does Microsoft get most of the hatred from the open source community? 
I guess if there's any one "incident" then it was the so-called "Halloween Documents", which were a series of memoranda that were leaked by a Microsoft employee to Eric S. Raymond in the late 90's, detailing Microsoft's desire to "disrupt the progress of open source software."

It is worth mentioning a fact that highlights the aforementioned statement: that Microsoft often engages in negative (non-technical) campaign against its competitors. One of the greatest foul plays in Microsoft's history is paying someone to write a book claiming that Linux source code was stolen from Minix, in an attempt to make companies afraid to use Linux, so that it can sell its own products, in the basis that it was not legal to use stolen source code. Fortunatelly, Andrew Tanenbaum wrote an article to refute the accusation.

While not so intensively, Microsoft still engages itself in practices like that, as one can see from the recent claim (in 2007) that Linux infringes Microsoft patents (1 and 2) or the more recent (2012)
"Droid rage feud" on Twitter. A link for the specific tweet can be found here.

While Microsoft's attitude has somewhat mellowed (compared to the past), many in the open source community still see Microsoft as a rather aggressive (and foul) competitor, particularly with respect to the negative campaigns and to the way they license their patented technologies (the "Open Specification Promise").

Now, whether that reputation is (still) justified is another question. Personally, I don't think Microsoft is as "evil" as some people would like you to think - certainly not compared to some other companies out there. 
