The are widely used and in a terrible format that's hard to work with (programmatically). So yes, there are problems.

My particular pet peeve is that many rendering platforms suffer from floating point rounding shenanigans, such that rendering/rasterizing a 8.5x11 doc at 300 dpi results in a the height being off by a pixel :/

PDFs and JPEGs are the standards for 'digital documents'. I expect they still will be in 30 more years because they're "good enough".

Other than plaintext, are there any others?