Debian is nice if you want to build your OS package by package.
Ubuntu uses the same debian package management but will install a much better basic OS for you then debian.
Ubuntu Starter Guide is a good place to start.
Wine will probably never leave alpha. By the time we get most win98se apps working longhorn will be out and nobody will build software supporting win98se. But SE4 works great in wine and thats all that matters.
Wine Application DB is a good place to find out if a program will work or not. You can also do a search with
Google Linux.