I'm strictly a Micros person so can't comment on Aloha or Digital Dining. I'm sure they each have a way to dump data. My personal preference is SQL, but that's just what I'm comfortable with. There's no "best way" to export and like MegabyteCafe said, as long as the data is there your IT team should be able to get it worked out.
Pasupport was partly right about the Micros stuff. The 9700 does use SQL Server, but as far as I know Micros still doesn't support accessing it directly. You're supposed to use some old 8700 functions that dump entire tables and then parse through the resulting files with scripts. Adding new objects to the database is a no-no.
There are also 2 versions of the 9700 you can buy. One has a watered-down SQL license which doesn't allow you to do much. The other, more expensive of course, version has a full SQL Server license. They still frown on accessing the Micros database directly, but you can add a database to hold and process totals.
The 3700 system uses Sybase Adaptive Server. Micros was pretty open minded about database access with this product, so you can write a query to get pretty much any info you want and dump it to a text file. You can also add tables, stored procedures, etc to the database if the need arises. Reporting in the 3700 uses Crystal Reports templates too, so modifying existing reports or makaing your own is pretty easy. This is my system of choice.