I've always been a fan of remotes with "hard button" over using the phone. It's nice to be able to pick it up and use it without looking at it. instead of trying to find an app, and the looking at the screen so you hit the right button.
you can use
remote buddy. It lets you customize the remote to work with any program. and comes preconfigured to work with many popular programs.
You can use it with an IR remote like the
apple remote or any of the programable remotes out there.
Or a bluetooth remote like a wii-mote or the newer harmony remotes.
full listing of supported remotes on their page
plus having an actual remote is nice when others have to use your system. they can figure out how to pick it up and hit play, as opposed to having to remember to hit the "P" key to play.
also look at
plex for a media server app, once setup it's pretty seamless to use to watch your shows and movies.