does it hurt game performance or enhance it? will HT cause issues in games? also i understand the OS and other apps can benifit from HT, so is there a way to run HT off only for game.exe's? if so how?

There have been other games that are negatively affected by HT as well, but they usually are not top rated great games. Shaun White Snowboarding wont even start with it on, RO2 had issues with it at first and the latest patch seems to have addressed those issues. For the most part, games that have issues with it are few and far between.

so leave it on and if i have any gpu related issues, chances are its not from ht right?

I have a X58 motherboard with an i7 and don't have any problems in game.
What probs. were you having?

It's not that games aren't made to support hyperthreading, it's that games aren't optimized to take advantage of highly multi-cored cpu's.  Hyperthreading is like a poor man's additional core: it lets one core that is not being utilized 100% do the work of two real cores.  
 
So, for example, if a game was optimized for two cores and you only had one physical core, but two logical cores (ht making it appear as two to operating system) with hyperthreading, I'd bet you'd see some improvement .... but not as much as if you actually had 2 physical cores.   But if you had four physical and 8 lofical because of hyperthreading, I'd bet you'd see a tiny bit of a decrease in performance.
 
Also, the performance is usually benched or measured when the only even mildly high intensity task being run is the actual game.  I'd be willing to be that if they did a comparison of HT vs no HT whern you had some stuff going on in the background (like compiling a program or unzipping some files or doing a backup of another drive or doing text identification of a scanned document or just keeping word, chrome and a handful of pdf's open or a cd /dvd ripping program or somethjing) you'd see the games derive more of a benefit. 
 
 The key is to put the game in a situation where it can't use the number of cores it was optimized to use as much as it can.
 
Keep it enabled unless it gives you issues on a specific game (as others said, I'd be skeptical about that being the cause) or you want to keep your temps down while playing a high quality game on a decent oc.