The key is full disclosure, in advance.
And I never had any trouble over it.
Additionally, I've found that at the point of employment projects don't need to be more than an idea; as long as you get them included with the contract, a simple abstract of what is covered is enough to give you something to play with whilst employed by said company.
Oh, and make sure to include projects even if you don't deem them to conflict with the company's area of core business. IME they'll be met with a chuckle and a 'not sure why these are here', but when the company is subsequently working out how to jump on the latest buzz bandwagon your side project may suddenly fall under some random wing of interest. Far easier to get it in there early.