Adv Task Killer and running apps

Personally I like EStrongs Task Manager best, followed by TaskPanel, then the others including ATK. The apps you mention are going to start up and keep restarting whether you kill them or not. I wouldn't worry about the stock apps too much. Only way to prevent them starting is to root and move the apps. Just add them to the ignore list so you don't see them and forget about it. It should be pretty rare that you need to manually kill apps to increase performance and autokilling is certainly a bad idea.

BTW, none of the programs I listed are pay so you should be able to try each yourself. But my take on four of them are:

ASTRO Process Manager. In my view displays the most useful information and has the most polished interface. For some reason it can tell you cpu, memory, and load very efficiently whereas ES below slows to a crawl if you enable statistics. Ability to ignore apps and remove from view and kill all non-essential apps. If you already have ASTRO installed seems to me the best bet as you don't need a separate app. I need a root file explorer so I uninstalled ASTRO a while back. One thing I don't like is that it shows "essential" apps in the app list but won't let you ignore them.

ES Task Manager. Similar features to ATK but I like the interface a bit better. Standard ignore list, remembers and highlights apps you've killed before, and one click kill all. Pretty efficient. Also allows you to kill certain things ASTRO doesn't, e.g. the keyboard, Google Search, etc., if you want. Allows you to manually refresh. Even though it has a services tab, it's read-only and seems a bit pointless to me. Also, will allow direct uninstall of apps from long press

TaskPanel. I like this at first until I realized tasks had to be killed individually. It seems to me it's really meant to run in auto-kill mode or to kill one or two specific apps.

ATK Free. As I said before, similar to ES but no service tab, full app lines aren't highlighted but uses check boxes, no manual refresh (might do it automatically but you can't tell), and the detail from long press is pretty useless. Doesn't show as complete a list of tasks as ES either.

I ignore apps that either seem to continually restart or I know are core: Alarm Clock, Voice Dialer, Pico TTS, Google Search, Settings, My Uploads, Android Keyboard, GV, my home (dxTop), Google Partner Setup, Messaging, any widgets, and any other app that you want to sync in the background.

In your case, I don't specifically know if Handcent needs to be always running to give you timely notifications since I don't use it. I would guess so. The other apps it sort of depends on whether you are expecting it to function when you're not actually using it. Do you want your IM client to notify you and always be checking in the background? Probably should ignore it then. If you only want it running when you're actually using it then it should be fine to kill. Navigation, for example, should be pretty obvious. If I arrived 15 minutes ago and am sitting down for dinner, it's probably getting whacked if I see it still showing in the task list.

You should also go through the settings of the apps you kill and see if they have some way to disable background syncing, notifications, etc. It will save you the hassle and battery up front.

Overall, unused memory is wasted memory, within reason. All of the ignore apps I listed above are what the average user is going to be switching between frequently. You want those in memory to reduce access time. Infrequently used apps like games, photo editors, nav and maps can be killed after use as insurance to make sure memory doesn't get too low. The OS should take care of it automatically but the fact that it has to at all will likely slow things down.