A guy that compiles the XChat GPL’ed code for Windows, at what looks like the official XChat site, XChat.org, tries to get you to pay for it – is that even legal? XChat2 is another guy’s build for Windows, and almost as up-to-date – use it instead.
The only configuration that drove me nuts out-of-the-box was the flood of “join/part” messages in large channels like #gentoo. From the XChat FAQ (at xchat.org, go figure), number 11:
11. How do I turn on Conference mode where I will not see join or part messages?
Right-click on the tab you want to change. In the submenu of the channel name, there's a toggle-item "Show join/part messages", simply turn this off. If you want to turn this option on globally, type:
/set irc_conf_mode 1
Then all channels you join after setting this will start with "Show join/part messages" turned off.