I have a mix (as you probably already seen)...I offer Premium Listings with logo or whatever, which show before the standard listings, but I only have a select few because these spots are for webmasters to take advantage of. I pretty much do what DD does, have them throughout the listings themselves. If there is anything I put focus on with paysites or affiliates, its generally in the homepage or other sections of the 'mainsite' areas.
I used to have another link directory a couple years back where I had all paysites and affiliates per category but had to go through them before you got to the actual site listings. It worked well, but didn't keep that concept when I sold it when starting 69toplinks.
If you intend to establish a LL for yourself, be prepared...its a lot of work.
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