Depends on your niche, etc.
If you're in a niche that caters to teens for example, you won't get a dime out of them more than likely.
It depends on your site, really. I know that's generic, but it's true. Ads aren't always a bad thing, if not plastered all over the place.
You can work out "premium" features, like additional theme choices, more storage space, additional plugins, etc. You'd have to probably code most of that, although there is a plugin that will get you started over on the WPMU Dev Premium site.
Donations are a possibility, although the return is usually low.
You also have to consider why people seek out a free blog host in the first place, when they could easily get a cheap hosting account and put wordpress on there themselves. Keyword: free.
There's lots of options out there, like "Feature X brought to you by sponsor", but those are not the norm. Usually it's enticing upgrades for more features, ads, or a combination of the 2.
Sometimes putting ads on the free accounts, and then a modest monthly fee (a few bucks) for ad-free and a few more themes to pick from works too.
Either way, it comes down to what your users will support. If they're unlikely to upgrade, even for a couple bucks a month, then ads are your only bet. Well, you could probably do affiliate links, but those don't necessarily pay well either.