Linksys routers aren't known for being able to use QoS or throttling very well. In my experience, trying to enable QoS on my WAG54g (closed source firmware) has only slowed stuff down, and I found that if I tried to run a torrent client on any machine on my network that it would kill the bandwidth to all other client machines even if the inbound traffic was well under my connection speed. Linksys routers are also known for collapsing under a lot of incoming connections (this is common with bittorrent), so that could be something to consider.

I've never used an open source firmware on my router but I've heard that decent ones are meant to alleviate this a bit, but still not really that well. Something else that could work is to try installing a level 7 packet filter to your router. That's similar to the type of throttling performed by ISPs. I dunno, maybe I'm just missing the plot, but this is what I used to tell people when I worked in support for an ISP.