1.The War is still ongoing. Snape appears to be a traitor to the light, but at the same time Harry & Co. (The order of the Phoenix, etc.) keep receiving highly accurate information that helps them fight ol' Voldy. Harry suspects it's Snape, but he is the only one who thinks so. The light has come up with a plan that will kill-off the Dark Lord and all his minions in one fell swoop. Can Harry find Snape before the plan is executed? If he does, can he convince Snape to abandon his 'post'? I'd like to see lots of time spent on the 'convincing' part!
2. If Harry had to choose between killing his enemy, Voldermort, and saving his lover, Snape, what would he choose? And how would he convince Snape it was the better choice? Ooh, more convincing!
3. After the war. Harry moved on with his life after taking a break abroad. Some years later he gets a letter from Headmistress McGonagall, summoning him to Hogwarts on a trivial matter. There he 'by chance' meets Snape and finds that even after the official pardon (Sev never got a medal) the ministry and other 'upstanding citizens' are harassing Snape with all legal (and some illegal) means at their disposal. It has gotten so bad that he can neither teach, nor brew, nor leave the castle; he is trapped. Harry to the rescue!!
All prompts can set be during/after any of the books you choose, but I do think would they fit better in the latter part of the series. I would <3 <3 <3 bottom!Snape and loads of angst!