Batman - Contagion, Knightfall are my two favorites but there's lots of great Batman stories, Killing Joke will give you probly the best Joker story.
Prof X/Magneto- there's an X-Men Classic issue #65 you can get for cheap that covers their origins pretty well, Xavier & Magneto vs. Baron Strucker & nazis. Fatal Attractions and Jim Lee/John Byrne's X-Men 1-3 put the two against each other, I liked both at the time, both are out on TPB.
Dr. Strange- you can probably get the whole sorceror supreme series 1-90 for really cheap http://www.comicvine.com/comic/doctor-strange-sorcerer-supreme/4049/&page=3 in the quarter bin. There's also a couple Essential Dr. Strange TPBs that covers stuff from the older (more expensive) Silver Age books.
Sinister- Inferno was his first big story arc you can get on TPB, Further Adventures of Cyclops and Phoenix (on TPB, can probly get the series somewhat cheap too) goes through his origin in late 19th century England & lays out his ties to Apocalypse, and Uncanny Origins #1- cheap 99 cent comic drops hints about his origin (as Claremont I think originally intended it) and his interest in Cyclops specifically
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