...I find this hard as fuck to ship. Despite my skepticism about how well they get along when forced to work together, at least within reason of the "Hero:Villain" relationship, I always see them as most likely being friends in their off time. Eggman seems to save him, despite lack of sensible reason to. So I suppose I can see a basis.
Edit: Sensible wording translates to "I don't understand, but I can see why. There is enough evidence of a lack of hate despite their roles."
Sonic walks in to eggmans base to find him half naked and lying on a double bed with rose pettles scattered round the place and a dim light shining* Sonic: hey babe! Eggyy: shhh no one has to know..HOHOHO!!! Eggman approaches sonic and picks him up and the and they and they....
Me: AAAAAH!!!!!! * WAKES UP CRYING FROM NIGHTMARE*