The Doctor having to mind-wipe Donna at the end of Series 4 (WHY????)
See why I said I pretend "Journey's End" ends after the TARDIS hauls Earth back to where it should be?
(Actually, my head-canon says that TenTwo didn't stay at Bad Wolf Bay, but he took up residence next door to the Noble household and becomes friends with Donna and keeps an eye on her without actually ever talking about their adventures. Or even that Donna's subconscious remembers her travels with the Doctor and she slowly is allowed to remember it and she doesn't burn up. At least that part of her mind remembers and she is still better for it. You can't run with the Doctor without it having some effect on you - even if you do have your memories wiped).
Seriously - I am NOT okay with how Donna's story ended in Series 4. "The End of Time" partially made up for it - but not entirely.