This allows you to specify options for a tracker, in all transfers, from one place.  You can open this window from Settings > Transfers > Trackers.

The first tab adds new trackers when a transfer is loaded.  By default, as of version 2.73, private trackers are not affected.  This can be controlled by using directives include_private and exclude_private on their own line, which will control the behavior of the following lines.

The second tab allows you to remove any trackers URLs that contain anything on the lines specified.  You can use a full URL, a domain name, or any sub-string that you want to match.

The third tab is the same as the second, except that the trackers will not be deleted, just ignored when the time comes to make an announcement.

The last tab can be used to control advanced options on specific trackers.  The first line is considered a "match" line, so you can put in any string here that is contained within a matching tracker URL.  The lines following it specify options for the matching tracker.  Then a blank line is used after the last option, and the cycle can repeat with another match line.

You can use the prefix regex: at the beginning of any match line to search for a regex instead of a simple sub-string search.

Option lines are as follows:

alias:(new URL) use alternate URL to announce
peerid:(new peer ID) announce with a customized peer ID
xfer_peerid:(new peer ID) set the peer ID of the torrent
cookie:(cookie data) announce with a custom cookie data
header:(encoded multi-line header string) announce with custom HTTP headers
xfer_created_by:(string) used when saving a .torrent file
replace_in_new:(new URL) upon transfer loading, will replace any matching trackers with the new URL
stats_report:all_time this is an obscure option to change the way the protocol bytes uploaded/downloaded is reported

Remember, the order is always match line, one or more option lines, and then a blank line, and then repeat the cycle.

If you need to bypass client restrictions on a tracker, please see the tracker spoofing page for an easy solution.