well there are atm two ways to have subs in mp4
1) the one described here, which means storing the subs in bifs format (which would btw allow using all sorts of funky designs for the subs (ie "star wars subs" (c) shitowax
))
you can create such subs with any bifs encoding tool available (ie mp4box, mp4tool, xmtbatch)
note that only mp4box handles .srt input directly! with the other tools you would have to transform the subtitle text by hand (as no automatic conversion tools exist atm)
2) nero recode2 adds the subs directly in the vobsub format to mp4, also atm only the nero dshow filter support playing these
but note that 3ivx is also considering handling these subs