There's also the Ghost Tower or whatever it's called in Lavender Town in Kanto, which has some tombstones in the town, as well as the tower being dedicated to dead pokemon. Also, in FireRed/LeafGreen, when you go to the Sevii Islands you can meet a kid who made a monument to his dead Onyx (I was recently finishing up my game of FireRed, hence why I know this).
Also if you want to read an interesting take on pokemon death as an actual game mechanic, read
this.
Oh and I dunno if you guys mentioned this previously, but if you never ever feed your pokemon (meaning you don't give them berries and whatnot), nothing bad will ever happen. However it is recommended that you spray them regularly with "potions."