Not too sure that access to the raw source code necessarily helps the situation greatly. To ensure interoperability of mods, particularly in a server environment while the game is still in development you do really need something like a modding API or master linkage mod like Bukkit.
The minimap mod (that shows top down view of the immediate landscape surrounds and lets you set way-points) is used by a number of players on the TOG server, and is the only one at the moment that I'm aware of that fairly innocuously adds to an individuals Single Player and SMP game, and as such we're accepting of. As a result I'm uninclined to make a sticky for acceptable mods presently. By all means continue to discuss mods in the forum in specific or broad terms - for example your A question of ethics...
thread has made for some interesting reading and viewpoints.