The philosopher's stone is an odd tool which has some uses, yes, but even that isn't easy to make, requiring a diamond and at least one trip to the nether for glowstone. I didn't actually know it could freeze water or solidify magma though, how does that work? Those uses aren't listed on the wiki.
You just aim it at water or lava and right click like if you were trying to transmute dirt/stone. Note that the aiming part is a bit quirky if you have a solid block close by, i found that taking a few steps back helped to target the liquid instead of the block. Oh and it can also transmute pumpkin blocks into melon blocks.
Note that i'm not against EE, i just noticed that when i played it, i was barely doing anything outside of my base. I think the problem is that since every ressource is interchangeable, you tend to stick to whatever is the most efficient way of getting EMC and do mostly that. I'm still using it, but i try to use it as little as possible when i play it with other mods, or many things would be too easy and boring.
The stuff i still use from EE : Alchemical bag+Talisman of repair, making charcoal out of coal, sometimes making a diamond when i'm stuck, and the philosopher's stone that i rarely use but is sometimes handy. Also i use the transmutation tablet to get rid of large amounts of cobblestone/dirt, or sometimes transmuting one into the other depending on my needs.