Top 10 - middle tier (Enlightenment)
There are many ranges to Tool, each one vastly different than others. From german rants about an edible/pastry recipe, to fist ####### (but not really), to anal sex (but not really), to embracing selling out, and the list goes on. But when they're at their best is when they self reflect. For some it's H. For others it's Right in Two. Or Wings. Among others. For me...it's these 4.
7. Pneuma. I didn't know what to think about this song the first time through Fear, but once my ears developed an expectation listen #2 got my attention #3 was jaw dropping and all subsequent ones move me in a way that nothing else in the catalog does.
We are spirit bound to this flesh
			We go 'round, one foot nailed down
			But bound to reach out and beyond this flesh
			Become Pneuma
We as humans have the opportunity to be so much more than the physical beings we appear to be.
Wake up, remember
			We are born of one breath, one word
			We are all one spark, eyes full of wonder
But it's on each individual to make the most out of the little time that we have. Will you conform? or will you reach out - beyond? Then when our time expires we will go back to being one again - only bigger and more powerful, but only to that level at which we allowed ourselves. Whenever I am having a bad day I am sure to get this song into the mix somewhere to recalibrate. And as 
@Pipes said earlier - the live performance...an online clip, words, or even the Danny Carey video I linked to earlier. It doesn't do it justice. You have to see it...feel it...experience it to truly get it.
6. Parabol/Parabola. Others have said it, but this is one song. Parabol by itself is a throwaway and Parabola by itself is incomplete. You need Parabol to lead into the meat (Parabola). Kinda like how I think Vicarious and 7empest instinctively ended up next to each other, I think the same about this and Pneuma. Pneuma is the macro - and this, the micro. 
Twirling 'round with this familiar parable
			Spinning, weaving 'round each new experience
			Recognize this as a holy gift and
			Celebrate this chance to be alive and breathing
			A chance to be alive and breathing
This body holding me reminds me of my own mortality
			Embrace this moment, remember
			We are eternal, all this pain is an illusion
I stole this, but I'm stealing it because it most aptly put what I think about this song - 'each gift of life in this world is to be cherished, don't give in to the pain and strife you experience; learn from it, and remember that it (life) is fleeting.'
5. 46&2. The theme of this tier is rather obvious, huh? Pneuma and Parabol/Parabola represent identification - and this represents the resolution. Or at least the path towards that solution. It's about growth.
My shadow's shedding skin
			I've been picking scabs again
			I'm down, digging through
			My old muscles, looking for a clue
But that you cannot attain that third level of evolution until you after digging into yourself - and cleanse. Everything about yourself that makes you uncomfortable. 
I choose to live and to grow
			Take and give and to move
			Learn and love and to cry
			Kill and die and to be
			Paranoid and to lie
			Hate and fear and to do
			What it takes to move through
You occupy your body. You control how it all works together. And every component must be working in conjuncture to successfully progress to that level. No matter how painful it is - and it will.
See my shadow changing
			Stretching up and over me
			Soften this old armor
			Hoping I can clear the way by
			Stepping through my shadow
			Coming out the other side
			Step into the shadow
			Forty six and two are just ahead of me
That last line. That last line gets me. Every single time. Because no matter how deep I dig. I always feel like I'm not quite there. That it is perpetually just ahead of me...
#4 Lateralus. ...as this song makes me understand why. I reach out to embrace the random. I over think. I over analyze. Black then White are all I see. Red and Yellow then came to be. I lose myself between the sounds. I wither my intuition. I miss opportunities. I am just one spark. My eyes full of wonder. This body holding me. I embrace this moment. I see my shadow changing. Coming out the other side. Forty six and two. Are just ahead of me.
Spiral out.