[Allithus]

about the ps2 version which i hadn't played but red a lot on and seen the ending on youtube

Spoiler for Tomoyo After and Thoughts:

I think tomoya's dead at the end and the very last bit(the part which shown tomoya and tomoyo holding hands) is just symbolism or dream. But it doesn't really matter whether tomoya actually died or not. but then again since ps2 version is a R12 game i thought maybe they changed it so a 12 years old can take it in.
from what i can see in clannad and tomoyo after, Tomoyo is emotionally weak and almost all the things Tomoya did in tomoyo after is to protect her mind, remember just before the "after" part Tomoya asked Tomoyo if she have the strength to go on if something happens to him in the future, i never expected it to happen at that time.