If you are still interested in ideas to promote lesser-known comics there's one big idea that hasn't been discussed: More categories.
People are most likely to be enticed into reading something not too far from what they are currently reading, so give them more options to find that. Anthropomorphic/furry comics is a common preference, or for some, something that ought to be filtered out of their searches. And what about 3D/CG comics? Some people really dig Flash/Poser/Other Tech stuff, and others disdain it. Make both options searchable.
Some people like comics that update daily, others want to savor a long-running weekly. Why not have (intended) update schedules as a searchable item? Some people also like comics with deep archives, so let that be added as search criteria.
And as tastes vary, so do standards. Some people do not want to be surprised by violent or racy content. Some people *only* like comics with gore or graphic sexuality. Some people like a middle ground. Give all the creators on your list a chance to voluntarily self-rate, and then make that searchable too.
In the end, a person should be able to search for a daily furry sci-fi Flash comic, rated Teen+, that's been around for a couple years or more. And maybe, just maybe, that will be their way of finding that hidden gem that has been languishing unnoticed down in the low 400's.
Seriously, *anything* has to be better than getting shunted back to the Top 100 page at the drop of a hat.