If you can stand the spreadsheet style of writing and the sheer number of giga-peta-watts, Nairda has a few interesting ideas.
B5: A New Beginning What if, after the Dilgar War the Earth Alliance higher-ups realized what an underdog the EA could be in technology and industrial output compared to the Centauri and other, older races? What if they decided to do something about it? What would the Minbari War look like if preceded by a decade of military buildup/preparation, exploration and expansion, and frantic reverse-engineering of alien technologies?
Stargate: Birth of the Federation When you think about it, the two Stargate shows (discounting universe, which hadn't started when this fic did) left on a pretty high note. Earth inherits the technology of the Asgard, Atlantis is sitting in San Franciso bay. All their enemies are dead, forgotten or uninterested in fighting except for the Wraith and, what? The Lucian Alliance? Don't make me laugh. So what's next?
How about full disclosure of the Stargate program and it's fruits, and the formation of a world government (the Terran Federation) dedicated to exploration and expansion, in a carefully planned, peaceful and basically benevolent way, of course. And the utter genocide of the Wraith. An interesting what-if.
Harry Potter and the Alien Reality for some reason there are an awful lot of Harry Potter/Stargate crossovers. This is one of the only two I consider worthwhile. Voldemort, aware of the Prophecy sends Harry to an alternate universe, the Stargate universe.
Harry Potter and the Ancient's Bane and this is the other one. Some Dr Who/Torchwood early on. Harry is John Sheppard's adopted brother. After the Voldemort issue is dealt with, Harry goes through the Veil in the Department of Mysteries which turns out to be a prototype Stargate leading to... guess.
Visited by a Doctor both the Doctor, and to a lesser extent the Master, take Harry Potter under their wing, popping up at odd points in his life to offer sage advice and helpful gifts, and setting him up for a life of adventure that will go far beyond Hogwarts and Voldemort. Draws very heavily on Classic Who, but you don't have to be an expert or have grown up in the seventies to enjoy. Except maybe the bit with the Fourth Doctor.
Formal Declaration AKA the Most Awesome Crossover Ever! In no small part because it's writer knew when to stop. Just read. Any description I could give would only detract from it.