Yes. But around the time of MGS3 somebody filed a lawsuit saying that the MGS theme was a rip-off. So the theme is very similar in MGS and MGS2 and then it got a reworking for MGS3 (but this new theme still used cues from the original one as well as using the MGS2 theme at the end of the credits for MGS3). MGS4 on the other hand did not contain any themes in the soundtrack using the old themes from previous games simpyl because they werent allowed to. Peace Walker unfortunately is the same.
http://www.joystiq.com/2008/12/12/metal-gear-solid-theme-unused-in-mgs4-due-to-plagiarism-claims/Aah according to this article nothing ever came of it, but Konami were obviously nervous about the whole thing and chose to come up with new themes for future games rather than risk a lawsuit (so far MGS4 and MGS:PW). So while you might hear the old themes on the walkmans or ipods in MGS4 and MGS:PW you never hear them used in the games soundtrack, neither as reworked versions by harry-gregson williams or as the originals.
http://www.youtube.com/watch?v=vYQQ1PZHF8UDont think they had a leg to stand on really when you listen to this, so they backed down and decided to come up with new themes for future games.
MGS theme by Tappy
http://www.youtube.com/watch?v=SIbP33Snm2AMGS2 theme by Harry Gregson-Williams. Notice how it takes a part of the original theme and makes it the main focus for the new theme, but its essentially the same theme, just reworked. The ending part is simply a slowed version of it, to make it more epic.
http://www.youtube.com/watch?v=QiPon8lr48UMGS3 theme by Harry Gregson-Williams. The ending to this is again, exactly the same as the MGS2 theme and the bulk of it, is still based on cues from the original theme.
http://www.youtube.com/watch?v=rNVCD1dsnJIMGS4 theme by harry Gregson-Williams. Still similar in style and tone, and doesnt feel out of place, but there are absolutely no parts of it where that revert to any of the original themes. Some of it deliberately tries to envoke the original themes without actually being the same.
http://www.youtube.com/watch?v=o9Pu92St5O0MGS:PW theme by ? Still inkeeping with the other themes, but again contains no cues from them, and its completely new.
http://www.youtube.com/watch?v=aL5C2lL6Cv0