I also have an excel sheet. Although I've never had trouble remembering which ponies I have, it's the accessories where I can get confused. The excel sheet has a tab for each gen, another for play sets, and another for my want list. All the ponies on the want list are already listed in their respective gen, but are marked in a colour so I know I don't have them. Then I just change the colour any time I add a new piece to the collection. I also mark down the pony's condition, and any special info (like if she was a gift from a friend or something). It's about my third iteration of a list, but this one seems to work for me.
Elf