Disk I/O Utilization at 95%
We had 2 problems:

1) We had one mysql query that used three joins. Turns out this function was crashing Mysql. We rewrote this query to use 4 mysql queries without joins and that solved that problem. (Bit of a hot-fix, we will probably rewrite the function so it is possible to cache it).

2) We were experiencing around 99.9 % I/O wait when we only used 10% cache Mysql only using 10% of cache . We tried to edit the mysql config (quoted at the bottom). This helped a lot but did not fix the problem. It turned out another user on the shared server was causing 99.8% I/O spikes. After contacting our server provider they moving the server to another partition and the problem was fixed.

table_open_cache = 1024 
sort_buffer_size = 4M 
read_buffer_size = 128k 
query_cache_size= 128M 
query_cache_type = 1 
tmp_table_size = 64M 
thread_cache_size = 20 
innodb_buffer_pool_size = 512M 
innodb_additional_mem_pool_size = 20M 
innodb_log_file_size = 64M 
innodb_log_buffer_size = 8M 
innodb_file_per_table innodb_file_format = Barracuda