JDownloader certainly messed it up (at least) at one time in the past... searching the net reveals quite a shitstorm of horror stories and even on their own forum you'll find a lot of confusion (and verbal abuse).
However, it seems to be slightly different than the first impression. They do add bundleware (just like Vuze and a zillion of other free tools) and (just like Vuze) the installer
should ask for each of it to be installed or not - which sometimes is pretty misleading and you need to read very carefully. This is how it
should be done and (at least) at one time JDownloader failed to ask and silently installed the crap. Reading the forums, the developers confirmed that - as a horrible glitch - apologised a thousand times and offered help removing the crap. As a result of this disaster they also seem to consider a "paid" version in future in order to gain income independent of advert deals.
I have no background information if it really only happened this one time or if the "silent crapware" mode was on multiple times. Some of the stories on the net are pretty weird and some seem to have multiple triggers. For example, some people are running JDownloader through a VPN, and since the developers have international deals (different adware for Russia, Asia, USA, etc) there were some further complications with suddenly some russian pop-ups on US computers, etc. pp.
One way or another - I'm using JDownloader2 for ages and somehow I'm dependent on it, because it perfectly supports simply *all* hosting platforms in existance, and you can let it run automatically with tons of links. I was recently forced to make a new install on a new machine, and with bad feelings I installed the "ad free" version from here, as recommended on their forum:
http://jdownloader.org/jdownloader2
All that I can say is that it definitely
did not install
anything without my consent and that the tool runs perfectly. This does not mean that it will do the same on other machines, but since the company wants to stay in business, it actually makes sense not to fool their "customers" again and again and again and again...
PS: And having said all this - if anyone is using Transmission (on OS-X), they never had "adware" but someone hacked them and version 2.90 included ransomware. If anyone installed it, you need to act
immediately or your harddisk will get encrypted:
https://www.transmissionbt.com/
This tool was always recommended because a) they had code-signing from Apple and b) "no adware"... so the end of the story is: If you install
ANY software you need to be careful in times like these, and a simple "adware = evil, no adware = safe" is no longer reasonable. Sadly.