Just seems very contradictory.
JDownloader: no. IIRC, it's actually officially sanctioned by the hosting sites. For example, the first time you download from any site, you're required to check a box in JDownloader saying you agree to that site's TOS, which means that JDownloader obviously isn't in violation of the TOS. And JDownloader very prominently displays links to premium account signups, so I'm pretty sure the sites like it. Like icebraining said, their primary revenue stream was premium account fees. Otherwise, they would be constantly changing the layout to break JDownloader support.
Don't get me wrong, I am a regular user of these kinds of software products, but just by their incredible amount of supported download hosts it seems that they are at best "tolerated". But I guess the tolerance level is also quite large in this "sector" as long as it doesn't target their premium account business.
This might have more to do with the quality of the software (a desktop Java app? in 2012?) than anything else. I would love for someone to come along and make a JDownloader clone using GTK or Qt.
That said, you're right in that JDownloader's in a gray area. They can't have possibly gained approval from all those sites.
JDownloader breaks our business model since we don't have premium accounts, but in the end you have no other choice but to accept that some people are leechers.
So, please don't think you're doing good when using tools like that and advocating their use.
That doesn't follow, at all. TPB could make me check a box saying, "I agree not to commit copyright infringement" every time I want download something, but that doesn't change the nature of what I'm doing.
Besides, even if MU had them, ads nowadays are paid-per-click; services only make money if you actually clicked on those ads. There's no real difference between using JDownloader vs going to the web page but not clicking on any ads.
> covered in adverts
If advertisements concern you, use AdBlock. Or use JDownloader, like I do, and avoid viewing the site entirely.
> long waiting times
If you created a free account, you would only have to wait for 25 seconds, better than the vast majority of other similar sites (MediaFire being one of the few sites that doesn't have a wait time). JDownloader alleviates this issue as well - it supports "logging in" to reduce wait times, and once you've passed it the link, it'll auto-start the download after the wait time.
> capped speeds
Nothing could be further from the truth. MU was one of the only sites that didn't cap speeds. Downloads from MU always maxed out my (24 mbit fiber) connection. Slow download speed is one of the biggest problems with the hosting sites that have remained online.
> no parallel downloads from the same IP address
Considering that it maxed out your connection, this didn't seem to be an issue. JDownloader again - it'll automate serial downloads of a large number of files.