So what would you say is the best one to use with Ubuntu? Going to change the window box i use for seeding over to Ubuntu when my new drive comes next week so need a good tracker client to use on it..

As you already know, I don't use Ubuntu.
However my favourite BitTorrent client is BitTornado. I find it flexible and it has the features I need.
Available for all my fav distros, I suppose it should be available for Ubuntu too.

See it is in synaptic so will give it a try then.
Thanks

I'm a big fan of Transmission.

Agreed. Transmission is hands down my favorite non-Windows torrent software. I have mine set up to monitor a CIFS-shared directory for .torrent files and queue new ones up new ones whenever I drop them in.

I prefer Transmission on any UNIX-based system.

deluge

I would say Deluge because is the most uTorrent like. Transmission is so simple for me.

rtorrent for me