1) What are the most common prices in your industry? If you aim for a smoother experience, it's usually better to stick to those. If, on the contrary, you want your price to really stand out, it's better to show a shocking number. And sometimes, a shocking number can simply be '$50'.
2) Who's your target? Consumers may be comfortable with $49.99, but Accountants will find it ludicrous...
3) Test, test, test... If you don't want to change your prices, at least you can test 2 different Ads (if you can reach your audience through ads, that is) or change the prices you show on your site (it's unlikely your customers will complain is they end up paying $49.99 instead of $50).