There are a few remote control apps for the pocket pc such as Vito remote. And I think most of them allow you to use custom remote files and save custom commands. The problem is the majority of the pocket PCs only include the IR for data which is fairly short range. In contrast the IR in remotes (consumer ir?) are much stronger and have a better range.
So if anything, you can try some of those apps first.
I think visual basic is supposed to be fairly easy for the pocket pc so if you wanted to build it from scratch its probably not that hard. I am not 100% but I do know one solution used to be send the IR signal through the headphone jack, so if you could get a IR dump to audio, then play the audio back through an IR led you may be able to do it that way as well.
This is usually when someone points out the fact that IR remotes are fairly cheap ~$6 but you might have bigger plans... IR signal to trigger camera, IR burst to trigger flash with ETTL data, based on events and time. Lots of possibilities and a pocket pc has a better display than an arduino. Google has plenty of data http://www.doc-diy.net/photo/rc-1_hacked/index.php