Hi BML
If you are considering listing thousands of sites, then at some point Links2 from Gossamer Threads will start having problems when it builds from the dbase.
For example, if you have a large Amateur category (and most link lists do) then because it is the first category to be built from the dbase it may start to slow down the build process or even stop. Several hundred sites in one category can start to really make the server work during an update.
Links 2 has limitations, although I know a couple of Aussie webmasters who have adapted it very successfully.
If you are looking for a long term solution which is robust and will not let you down, then Link Admin is the one.