How to keep a clean install with migration assistant

I have a mid-2009 13" MacBook Pro (5,5 - Intel Core 2 Duo - 2.26 GHz) with 8 GB RAM. I am currently running on OS 10.6.8 and want to upgrade to Yosemite.
I also plan to replace my original drive with an SSD.
I have had a series of Macs going back many years, usually getting a new one every few years and migrating everything from the old to the new. My Macs always start out fast but start slowing down within a short while. I was told this could be due to the fact that I am importing a bunch of old stuff onto my machines and that it would be better to keep the old stuff on a separate drive.
So I want to do a clean install of Yosemite and the small handful of other apps I need.
I will pull the original drive and put it in an enclosure and can either use it or my backup via Time Machine to migrate my files to the SSD via Migration Assistant.
What I am unclear on is what all I will want or need to migrate over, and what I want to avoid. I will bring my documents folder of course but I want to be careful not to bring over any unneeded apps, preferences, libraries, etc. Are there any resources for guiding me through the process? Is Migration Assistant the best tool for this?

Setting-up a new Mac from an old one, its Backups, or a PC

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