I use 75% (TypeMatrix 2030, Noppoo Choc Mini, thinkpad keyboards) and symmetrical ergonomic keyboards (ErgoDox, my 120key Access-IS keypad).
I usually miss dedicated Insert and Menu keys, because I prefer to use Control/Shift + Insert for copypasta (GNU/Linux user) and Menu is nice, when I don't want to reach for a pointing device, but can't remember some hotkeys/shortcuts.
I sometimes miss quotation marks, brackets and similar symbols present on the "cropped" keys that aren't present on my symmetrical ergonomic layouts (on ErgoDox or the POS keypad). It's only a matter of getting used to pressing a modifier to access an extra layer though, and then it's actually much nicer than reaching for those keys, and especially much nicer than reaching for the other frequent keys like Shift or Esc.
Nothing to do with moving to smaller keyboards, but I occasionally use some vintage keyboard, usually full-size, but winkeyless. Then I miss AltGr in the spot right under my thumb. As a Colemak user, I miss Backspace in the Caps Lock spot on ordinary QWERTY keyboards too.