I use Links for one of my sites and I intend to use it for a whole series of sites I've got in the works.
Links 2.0 looks to be a much better version than 1.0 - faster and better and more feature complete. The author was inspired by www.cgi-resources.com when he wrote it
There's also a program called indexfinger http://www.indexfinger.com
but I don't get a warm and fuzzy feeling from the programmer of that script. Something feels different with that guy. Plus, you can try the full version of Links for free and pay only if you use it commercially, after you've got it all set up. Indexfinger costs you money before you even get a full version.
Also, Links can be set up to use an SQL database for speedy searching on LARGE indexes. The pages are static, built by the Links script when you want it to, rather than building each page every time it's accessed, so that reduces server load considerably.
I like it