Hi there, I would not pass myself off as an expert, but I've been using an IPAQ as a remote for a couple of years now, and I'm looking to replace it with an X50v at some point in the near future.
There are several applications you could choose from, each with its own supporters and doubters. I'm currently using PDAWin which is a Pronto emulator. Does the job, but there has not been an upgrade for a good while, and by all accounts technical support is non-existant. [Link: pdawin.com]
Total Remote works in either native mode or as a Pronto emulator. The vendor at least watches this forum, and seems genuinely interested in supporting the customers. With an X50v you would not have to use the audio/IR convertor.[Link: griffintechnology.com]
NetRemote is in someways the new kid on the block, at least for direct IR. It was originally designed for controlling a PC over Wifi, but direct IR was added last year. Uses the Pronto CCF interface. http://www.promixis.com/
From my point of view, the three above are the most interesting, as they share the CCF interface which defines the format of your remote control. The are great examples of CCF files on this site, with a general recommendation to borrow one that you like and then adapt it to your own needs.
I'm sure others will add other applications.......... (cue)