Power down your routers/Airport and modem too. The routers cache DNS I know for sure, not sure about all modems.
I'm pretty sure Cocktail doesn't clear the DNS cache. I don't know where the DNS cache file is, never have manually moved it. I think the DNS caching is deep in the system somewhere.
So the average Joe should mucking around in Terminal? What's wrong with a GUI.. that's why we have them, isnt it? To make it easier than CLI.
I prefer a GUI also but what I mentioned is that Cocktail allows too easy click and go access to things that you shouldn't be doing if you don't know what they are for. I like it for certain specialized things that I need once in a blue moon, but in general the OS takes care of all of that prebinding, launch services etc crap automagically anymore. I can't remember the last time I needed more than font caches or system/user caches cleared. The one thing I do on a regular basis, especially with designers, is clearing font caches. I just use FontFinagler, it does Adobe MS and Quark caches like Cocktail does, but lets me pick and choose which ones I want to delete. It does one thing and does it well.
The other item I use is Lion Cache Cleaner.
Clearing localizations I've seen cause problems numerous times, and in these days of huge HDs the amount of room it saves in negligible. Messing with permissions and ACLs should not be done unless one really knows what they are doing.
Clearing cookies will cause you to have to log back in to some sites, an inconvenience.
Disabling sudden motion sensors and disabling journaling I see no reason for and are safeguards that shouldn't be disabled, and watch what you do in Network also. the only reason for disabling journaling might be to speed up HD access if one is doing massive video crunching or something, but in general is a good thing to have on to keep the HD healthy.
I gave you the terminal command so I'd hope you'd trust it.
The main thing you have to worry about in Terminal is if one is using the rm command to delete files, that is something you can't undo.