I am not sure now which subtitle types are working and which are not. With subtitles recorded with EyeTV via a digital source (not with EyeTV encoding them itself) in Europe, an export from EyeTV will keep the subtitles. Once I have passed that source through Toast, I lose the subtitles. Which subtitles are you able to view still, and where? If the subtitles that are recorded are actually burned into the original image, these will export since it is part of the image. If they are a separate subtitle track, I haven't tried exporting these to my iPod, either using Toast or direct from EyeTV. iPods should be able to display "closed captioning" (the US version of subtitles) though it may only be able to do this on an external screen (set Captions to Display as On). MPEG-4 does have a text track. The question is, how do you get the subtitles to go to the text track in MPEG-4, and even then, is that the track that the iPod will use to show them, and will it show on the standard screen, or does it need an external one, or does it need a special US-style closed captions track, or will it work with a European one?
From regular use, I know that Toast normally just ignores separate subtitle tracks in Europe, unless it is working out how much space it will use, in which case it includes them in the calculation, then discards it anyway (meaning the predicted space is less accurate). You could try taking the subtitle track and then burning it into the image, then export it to iPod. As far as I know, Toast couldn't do this for you, though I think that Final Cut could do this for you (bit of a big hammer to crack a nut, though). I know that VLC can display them, but I have never tried hard burning them into the video file. You could try Handbrake, since that is open source and does convert DVD to MPEG-4, so it may be able to do the job. It would miss out Toast altogether, but if you are using Toast to convert from EyeTV to iPod there are too many steps there anyway - EyeTV should be able to do it directly. If you want it to add in subtitles, they are in the wrong format and Toast is ignoring them, so that, unfortunately, won't help you either. Let us know if Handbrake does anything for you.