I know the 3.0 starter box came with tokens; I still use them actively. There were also a number of issues of Dungeon that came with tokens; looking at them, I think they were for 3.0 as well, since some of the monsters aren't square (even in the last set that I have, the ankheg is 5 feet by 10 feet). I believe that there was also an issue of Dragon shortly following the 3.5 release that came with tokens of dragons of various colors in the new 3.5 square dimensions, but my family kept the Dragon collection when I left for college, so I can't confirm.
But yeah, I don't know if the 3.5 MM came with tokens, or where to find some if it did. We just kept using the 3.0 MM and the SRD.
Or, just
roll your own. Pull art down from the SRD, slap a border and some numbers on it, print it, cut it out, and stick it on a washer. Boom. While I haven't actually done this, I did build a library of pogs for
GameTable with most of the SRD monsters in a couple of days over the summer. Wasn't hard, was kind of fun, and now if I do need tokens for a beastie that I don't have, I can just print and cut out the pog (the washer seems kind of like overkill; I have other paper-only tokens that I use sometimes, and the lack of weight is usually non-problematic).