If you are ok working with divs and style sheets, there is one that has been around for a very long time with a company called
Gossamer-Threads which has two program (CGI) scripts:
- Gossamer Links (This is their mainstream links script)
- Links 2.0 for $150 but I think you can use this for free - might want to confirm this though and its upgradable to Gossamer Links. Dont let the drab default style of it scare you, its very design flexible.
As theboyzlist mentioned, you also have k-links as an option as well. There are a ton of free scripts but if you are serious about running a link site, make sure which ever one you go with, make sure there is a good track record with them and good support network (this is so critical).