Dirk's point is a good one though, unless there are some people willing to do something besides just post on the forums about this it's unlikely to matter one way or the other. I will try to pull a draft together based on the various threads we have had in the past but I will be sorely disappointed if those of you who seem to care about this stuff are not willing to wade in and fix it.
The things can think of off the top of my head are datamodel create scripts, using namespaces, seperation of markup and code (and especially removing tcl from .adp files), package structure (which mostly needs to be updated, to be in line with tip 12), the ad_proc, ad_page_contract, ad_library javadoc tags, and declaring things public or private.
Also, I think we need a TIP for how we are going to remove deprecated functions (a la set_form_variables_string_trim_DoubleApos and util_PrettySexManWoman), since I would really like to clean out some of the really crufty stuff. I think remove anything two releases after it is -warn (i.e. remove the 4.6.3 -warn things in 5.1 and the 5.0 -warn things in 5.2) but that is probably something we need to talk about more and make a formal decision on.