Ok, here is my two pennies worth about irc servers.
I've been using the Unrealircd betas for sometime and it works well. It has many features that I find useful as an oper and as a user. However, some people say since is it still beta that it is still full of bugs and crashes under heavy loads. I haven't stressed my server so I wouldn't know. I've been running it on Slack 9.0 for a long time and haven't had it crash on me yet if that says anything.
I've also tried Ultimate ircd, which is a good server in my opinion, but it doesn't seem to be under much development lately and therefore there hasn't been many updates and doesn't have the features that I want.
Also to mention is bahamut (dalnet), hybrid (efnet, I think) and the many others that people have coded or modified in some way. There are many, many irc server programs out there. I would say that all the ircds are command line, but there are some plugins for unreal to webmin, I believe, that you can use to set up the config file (I haven't tried it so I can't be sure). The best thing to do is do a search on google, sourceforge, freshmeat, etc and try the irc servers out and find the one that you like and works the best for you. And be sure to RTFM all the time.
Next you will need to look into services for the ircd (if you want Nickserv, chanserv, etc), which is a whole different ball game. Anyways, good luck. If I have said something wrong in this post, I'm not a expert by anymeans just trying to help out.