IMHO option 1 is the best one, we already have rAsql that makes extremely easier to use mySQL so I don't think anyone will have difficulties exchanging TXT servers for SQL. Plus this option would help a lot on db editing (using some tool like phpMyAdmin), creating new entries will be muuuuch easier, but it's also needed to release a db converter because there are lots of customizations available converting them manually would be a very painful job if you know what I mean.
I don't agree on converting configuration files, there're too many important commentaries there as Aeomin stated.