Whilst I keep rerolling alts trying to get my season off to a start I keep saving all my chipped gems n upgragding them in my cube.
Is there any point to this?.. whenever I play a public game nobody ever picks them up haha. Is there any real place for perfect gems in end game or am I wasting my time?. I’ve devoted a whole stash tab to them n skulls
Chipped gems are used to transmute runes from Thul(topaz), Amn(amethyst), Sol(sapphire), Shael(ruby), Dol(emerald), Hel(diamond), whose drop quite frequently in Hell, opposite to chipped gems. Also, you need higher quality gems to transmute runes Io+, the pattern TASRED repeats.
Perfect gems are used for crafting, re-rolling iLvl85+ charms(this is the major usage of gems for me), and perfect topazes are cheap way to create decent MF armor and helmet.
You can use them to reroll Baal/Nihl/Diablo Hell grand charms for those +life skillers. Save your PAms&PRubs for crafting Amulets&Rings gambled at lvl 90+.
(Ideally 93)
skulls can reroll diadems for that +2skill +20fcr rare. i also use skulls to reroll rare lvl 9 jewels for pvp
use pgems to reroll baal charms.
if you find a grand charm from baal, you know its highest item level and it can give you +45life.
so you reroll it and hope you get +1 skill +45 life and have a GG grand charm.
as a sidenote, if you find a GC with +45 you can sell it as such, because the stat itself is proof that the GC is max level.
also crafting rings or amus takes quiet a bit of pgems. as someone else said people us skulls to reroll dia.
all this stuff is endgame! 
hope it helps.
I generally keep 1 of each type of chipped/flawed gem for transmute recipes, and re-acquire them if I use any of them. Otherwise no there’s little point to transmuting gems up since Flawless gems are plentiful and easily acquired.