Migration Assistant vs Manual copying from bootable Backup?

I installed SL on my mbp and used the Time machine backup to migrate my user/apps/settings.
Initially it seemed to have worked fine... but then when I started using it and I realised that some of the versions of apple apps like "preview" had been downgraded to older versions... not the new version that came with SL (in previews case it should have been 5.0, but Mig *** put it back to 4.3 nothing could open with it).
This happened with a few apps and other things and the whole system didn't seem to be very quick... not like when i tried installing SL by itself without migrating anything over.
So I decided to copy what I really needed over manually... Mail/Address Book/iCal/Stickies Database/iTunes library/iphoto and a few 3rd party bits from user/lib and user/library/application support etc.
This is so much better... I'm sure it has lots to do with other 3rd party apps not bogging it down now with old lib files. I've re-installed most apps i want like office, toast and logic studio 8 and now all I need is for Pro Tools to get their act together and update their software.
What I wanted to ask is what the best way to copy over everything manually is? There doesn't seem to be anywhere that has a guide for this stuff... everyone thinks migration assistant is the best... but after a clean install it copies lots of things you don't want... and that defeats the whole purpose of a clean install!
I just don't want to copy anything that might be old and unnecessary over to SL. After I copied it all over only Mail showed that it was updating any databases or anything... all the other apps just loaded and that was it.
The reason why I'm asking is that down the line in a few days or weeks I know I'm going to realise that I haven't copied something or my old skype chats have dissappeared (which I managed to realise already) or some other app has lost loads of info I used to have.
Here's a list of the apps I use:
All apple apps
iLife
Pro tools M-Powered 7.4 (which seems to work through the migration assistant way)
Logic studio 8
flip4mac
google earth
handbrake
MS Office 2008
Skype
Toast 7
VLC
youcontroltunes
I'm sure you won't be bothered with telling me how each of these work, but if you could point me to where they keep their important files that would be great.
Thanks for your help.

I would use migration assistant and the clone. [Check this read out|http://support.apple.com/kb/HT3322]. You will be asking for a load of trouble if you try to copy everything by hand, although Superman could do it. I'd use migration assistant on data and apps, but not on users and settings. Before, I would uninstall any incompatible apps. Use these lists to check on incompatibilities: [Here|http://snowleopard.wikidot.com> and [Here|http://snowleopard.wikidot.com>.

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