This is one of those \'oh my god\' moments.
The previous programmer in our company has left behind a badly-coded application using PHP and MySQL.
One example
So you're saying you want a query that returns all rows where a user has a specific option?
Well, ugh...okay, this isn't pretty, but you already know that, so:
select * from user_table
where concat(',',option_field,',') like "%,option_you_want,%"
I can't speak to the performance impact--it's likely not pleasant, but I think your other option is to break out the row into a separate table, but you're saying that's not realistically available to you.