the issue with town killing has always, and will continue to be, penalties that are not severe enough.
if you want to hang out in any of the towns, you should be FORCED to play safe. i am a huge pk and i thoroughly enjoy killing noobs in towns, around towns, etc. this would negatively affect my character, so i am not just some carebear hoping to make my life easier.
this thread is basically one giant suggestion that would only serve to improve the immersion and feel of the game. although, i will have to disagree with keldorn... if it starts becoming like wow where people hang out in front of towns with their buddies in their leet gear, there won't be much of a population for long! if anything the top end gear needs to be even more rare because most players who care to have a nearly endless supply of t3 gear that could only be depleted through non-normal means of dying... eg, chain deaths before the end of the wipe just for shits and giggles.
IMO, the protection of towns should extend to the immediate area they surround. If you kill someone in an encounter with marauders and NCR patrol, you should still take an NCR rep hit. Likewise, in the boneyard, I can't tell you how many times i've killed people in plain sight of the regulators, only for them to basically congratulate me on the kill and then try to steal the loot themselves. am i wrong in thinking the regulators by FO lore should be shooting me and helping my victims, not waiting to steal my loot?
if there was a 'localized' justice system, not wasteland-wide, i think the game would drastically improve. Also, being killed by someone should auto-red-name them for you... you can set them green yourself at a later time if they prove to be non-hostile.
like others have said, there is no all seeing eye that judges the actions of all in the wasteland so a blue/red PK/APK system like UO would not work. however, i do believe a local justice system is exactly what is needed. if i am PK in the boneyard, i should not be allowed into adytum. likewise if i am a friend of the regulators, i should not be permitted into the gun runners. (wait, i might be wrong. i think the gun runners are hostile to adytum, right?)
noob gankers with their 5-6man TB-encounter traps outside NCR should suffer the penalties of their actions. there is no cohesive feel to the areas around the towns, they feel as though the NPCs in those areas are completely disconnected from the main areas.
TC towns should probably be exempt from this rule, but with enough balancing of both NPC strength and penalties, you could apply a blanket, localized rule to all towns that affects the immediate squares surrounding such a town.
on that note... the squares between hub and JT are the most dangerous in the entire game. the hub patrols there should be FEARED, not looked to for an infinite supply of 5mm and assault rifles.