There's no problem with glibc and uClibc living side-by-side with some programs linking to one and other programs linking to the other. However, there is a problem with additional libraries. Each shared library on your system will be built against either glibc or uClibc (using the corresponding headers, which define distinct ABIs for the standard library functions), so for example if both a glibc program and a uClibc program need ncurses, you'll need to have two versions of ncurses built, and have a way of ensuring that the correct one for the given program gets loaded at runtime. Alternatively, you could choose to only use one set of shared libraries, and use static libraries for programs linked to the other libc, but you'd still need to build your 2 sets of libraries.