In my experience there are two places where we want to use uint8_t to mean 8 bits (and uint16_t, etc) and where we can have fields smaller than 8 bits. Both places are where space matters and we often need to look at a raw dump of the data when debugging and need to be able to quickly determine what it represents.
The first is in RF protocols, especially in narrow-band systems. In this environment we may need to pack as much information as we can into a single message. The second is in flash storage where we may have very limited space (such as in embedded systems). In both cases we can use a packed data structure in which the compiler will take care of the packing and unpacking for us:
#pragma pack(1)
typedef struct {
uint8_t flag1:1;
uint8_t flag2:1;
padding1 reserved:6; /* not necessary but makes this struct more readable */
uint32_t sequence_no;
uint8_t data[8];
uint32_t crc32;
} s_mypacket __attribute__((packed));
#pragma pack()
Which method you use depends on your compiler. You may also need to support several different compilers with the same header files. This happens in embedded systems where devices and servers can be completely different - for example you may have an ARM device that communicates with an x86 Linux server.
There are a few caveats with using packed structures. The biggest gotcha is that you must avoid dereferencing the address of a member. On systems with mutibyte aligned words, this can result in a misaligned exception - and a coredump.
Some folks will also worry about performance and argue that using these packed structures will slow down your system. It is true that, behind the scenes, the compiler adds code to access the unaligned data members. You can see that by looking at the assembly code in your IDE.
But since packed structures are most useful for communication and data storage then the data can be extracted into a non-packed representation when working with it in memory. Normally we do not need to be working with the entire data packet in memory anyway.
Here is some relevant discussion:
pragma pack(1) nor __attribute__ ((aligned (1))) works
Is gcc's __attribute__((packed)) / #pragma pack unsafe?
http://solidsmoke.blogspot.ca/2010/07/woes-of-structure-packing-pragma-pack.html