in general it is not a good idea to put a laptop in your legs, many models take air from the lower part of the laptop(where your legs are) and then release hot air on the sides
flash is horrible in linux so this is normal, it eats too much cpu and gpu so no solution unless everybody abandons flash
ati/amd combination is usually the coolest combination
i have heard that intel/nvidia from multiple vendors had many problems with temperature and chips basically detached from the mainboard(nvidia and intel too hot)
recent models hopefully doesn't have this problem but in general nvidia runs hotter than ati
the one that runs cooler is intel integrated solution but this one usually makes the cpu run hotter and you are just changing the position of the heat source
ths is form the temperature point of view
from the support angle, drivers, everybody will tell you that nvidia has better support than intel or ati so this should be taken into consideration but to be honest, the temperatures you mention are basically normal for a big cpu/gpu laptop
lots of users just will tel you that you should one of these
laptop coolers