Pagination vs ID sequence gaps

I’ve Googled this issue like crazy and I’ve come up dry…

How on earth on do you get pagination to look at the actual ID’s of MySQL entries instead of following PHP’s generated numeral ordering?

I have a CMS where the user can add and delete entries, however when they delete them, this of course, leaves gaps in the ID order. Far as my pagination knowledge goes, my script tells it to +1 after each ID to get to the next entry.

Any suggestions would be most appreciated.
Thanks guys