An iPod Touch/iPhone/iPad all can play FLAC files with a third party app.
The above recommendation of FLAC (the app) is a good one. Another is Golden Ear and YAMP is another. Thus far, none of the above have wowed me. The first two can do 24/96 and 24/192 (not sure if they downsample to 96). The major issue with these apps is that compared to the presentation of the native iTunes app, they all pale in comparison. That said, it means no transcoding to get your FLACs on the device.
Given the seeming shortcomings of reading the various metadata files, I would really prefer if any of the above apps would provide a directory tree view, rather than attempting to act like a database management system for the music.
Of the three, I use Golden Ear the most, if only because FLAC was having some major issues (but far less than those of YAMP). The former two are often neck 'n neck in terms of patches. GE had the better interface for a bit, but again, back and forth. They are both in the $10 range. Not brutal, but for apps that aren't all that polished, I find it tough to swallow. If I REALLY have to have FLAC, I use a Hifiman HM-801 or a Sansa Clip+
For regular iPods, anything 5G and upwards can't be Rockboxed (as of yet).