I know i'm late here, but getting back on the topic...
Most popular for me by far is FF7 for the 89, currently with 36486 downloads (the 92 version has 8419 on it if you were curious). It should be higher, but ticalc.org for the longest time had version 1.3 and 1.4 in the archive at the same time, calling the other file 1.3 version (modified). The (Modified) suffix was added when TipDS added the map function in the 1.3 code, which I adopted in the 1.4 code. I finally got it fixed when they started consoldating programs in the archive but I could never get the Modified tag removed from the 89 archive. For the longest time, it was #1 in the 89 basic archive. It would still be #1 if Ticalc.org didn't screw up the stats for the current #1. The current #1 includes ports for all calculators, so Ticalc.org decided to link all of the archives to the Ti-89 file, so if you download the program in the Ti-83 archive, it doesn't count for anything in the 83 archive but it counts as a download for the 89 archive file. Basicially, all the Ti-89 basic programs are competing against every basic archive that contains this program. I could almost swear Ticalc.org has it out for FF7, but that just my paranoid self talking
#2 was tetris for the 85. It currently has 10200 on it, it's probably dropping because someone modified it to have a better graphics scheme, not to mention the Ti-85 and it's OS varients are all but dead to TI now.
#3 is Gorillas for the 89, with 8643.
Many of the other games I have out there, have much smaller scores. KCHS Punisher IV's only got 2348, and with all three punisher games combined, barely break 8000. Both Icons Program Managers bearly break 7500, and all the stickman collections break 8000.
On an unofficial Note, NPO Vs Hays scores a 3579. Technicially That's GOD's highest downloaded game. It's also his only one
http://www.ticalc.org/archives/files/authors/0/13.html