On my server all commands are logged of course, but better safe than sorry. A corrupt admin could simply get a player's IP, which would pose a serious security issue. That's why I roll without applications. It's just advice though, no judgment intended.
I would strongly advise against allowing staff applications. On my server all staff members are chosen by a higher ranked staff member. This way you don't have posers who apply simply cause they like to abuse their powers.
Look at the offender's IP, do a simple whois, make sure it is not a proxy they joined from. Then simply contact the ISP to tell them their customer is engaging in illegal activity. In some countries, such as the Netherlands, a simple DoS attack can lead to 1 year prison sentence.
Typing ipconfig will return your internal IP address. This cannot be used by others to connect. http://www.whatsmyip.org/ is a good website to find out what your external IP address is. Then simply add the port to it (the port you set in the server config, 25565 by default) in the format ip:port, e.g. 127.0.0.1:25565
I think he means he made it appear very professional, whereas his management of the server may be amateuristic (not saying it is, just leaving the option open).
Plugins such as Grief Prevention and WorldGuard are compatible with Factions and neither one overrides the other. You need to have terrain editing permissions for the land of both the faction you are in as well as the region for World Guard or area for Grief Prevention.
This can come in handy if you have an area that you don't want your fellow faction members to touch.
You did this right. I suggest you switch to Herochat even if you are not interested in using the different channels. Herochat supports more variables coming from different plugins, such as Towny and Factions.
IGN: Lagado Skype: will PM you as you said Hamachi? Yes Why should I choose you? I make videos for YouTube so the entire match would be recorded, at least from my perspective until I die. I preview of my kind of commentary can be found on http://www.youtube.com/user/LagadoMC.