First off, I think its worth mentioning that no software will use your proxy/tor unless you tell it to. There will usually be some setting where you can fill in the proxy details. Sometimes you can set system wide settings, but I find those don't actually work all the time.. so be careful. If you just want to browse secure, using the tor bundle works great, it'll include firefox and is missing all those annoying plugins that might leak your info.
You could setup tor as a transparent proxy so all traffic gets routed through tor, in this case your applications aren't even aware they are being proxied. https://trac.torproject.org/projects/to ... arentProxy
has some instructions but they're linux/BSD only but I'm sure you can find a way to get it to work on windows.
Other then that you could setup a middlebox, imagine it like your router doing all the tor stuff for you (infact with some tweaks and depending on the type and brand of your router, it can do exactly that
But remember, tor is slow.. really really really slow. Its not meant for big files and so you shouldn't use it for downloading.
Not just because it'll be slow, but because you're wasting valuable resources and kind of ruining it for the rest of us(don't be a dick). So if you want to download stuff or torrent, use one of the many many VPN providers out there. But remember, although a lot of them claim not to keep logs, some of them do
. So be sure to checkout which is right for you.
Other then all that, please remember that you are not the only person using these services and so a lot (if not all) have been abused at some point. As a result, a lot of places will not allow or limit users using a proxy.
For instance, you cannot use tor, any known proxy, or any host linked to abuse on HTS irc.
We don't share your ip with others(and don't allow illegal activity) so you are safe to connect to us without a proxy.
There is far too much abuse if we allow them, people would be unbannable, flooding, spamming etc etc.