PHP/Filesystem
wins on speed hands down..
with a Sql server you have to open a socket etablish a connection, authenticate, break and package data up into TCP packets, recieve TCP packets, combine them into data, requery for bad or missing TCP packets, then reinterpret the SQL information into use able PHP form... all done behind the scenes of course
with a file system you just pump data to, or pull data directly from the local filesystem
but asking that misses the whole point...
Sql doesn't just store information it lets you perform complex Queries on it, it joins tables and selects out only the portion that you want...
lets say you are serching for a record in a flat file... one record per line, with a 10,000 records.... you have to read every single record untill you hit the one you want.... and you have to lock the whole file while you are in it, blocking any other process from co-performing a search.
with Sql it will find only that record you want. it will know where it is and find it directly, and allow others to read and write to the table at the same time....
if you are just storing 'Dumb' data on the system, feel free to use files, they are faster
if you will be wanting anything more that read and write diretly from and directly too the data, use a RDBMS like MySql
for instance you are better storing configuration information in files, since this information tends to be not changed often, and has no need to be searched or combined with other data, you just read all the time.