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There isn't a way to breach this limit legitimately on the iPad as far as I am aware, and since you are relatively new around here, please make sure you understand our rules. We don't provide support to folks who choose to pirate or steal software. That is not why we jailbreak here at iPadForums.
From memory I think there are some (approximately) 42,000+ packages in the default repositories in Cydia, and the APT limit is 65,535. Adding an additional 20,000+ packages legitimately is almost impossible IMHO.
The only way to fix this problem is by removing all the unnecessary sources from Cydia which are likely duplicating the thousands of legitimate packages in the main repositories. Then refresh the lists again.
For the record, I know of one lay to legitimately hit that limit. I run a custom repo that is hosted locally that I keep updated with the packages that I and my fiancée use the most often to save bandwidth (one download vs 7 for most items ) and as a result we hit that limit because of some of the custom packages I have developed as well. I had to start combining some of the custom packages to get things working again