I really like my 1993 GS500E but I could use a bit more power, does anyone know if a 2001 SV-650 engine would fit on my GS frame? Any known complications, issues?   

Ummm... NO

Not even close. If you want more power buy another bike 

Oh not a problem at all ... I fitted one ... in fact 2 just last week. Before that I put a hayabusa motor in it. 

BTW what do you hope to gain with it ... SV already is the same weight, has better wheels and in fact the suspension on the SV while crappy, is still better than GS, better brakes ...
You stuff an extra 20 hp in the GS and your wheels will fall off, suspension will bottom out (even more than it does now) and ...
Ohhh .. you'd put SV shock and suspension on the GS, then rear wheel ... swingarm too maybe ... After you do all that, the result will be over 50 lbs heavier than the stock SV and even as a photoshop will look like crap.

Cool.
Buddha.

 I'm talking a 650 not an 1100 ;o)  Thats why I came to you guys, knew I'd get the straight poop.  I'm a Newbie and not engine savy at all, any engine. Some one local was selling a SV with no title pretty cheap so I thought I'd ask.
  I just ran The Dragon @ Deals Gap and felt like the next size bike would have been nice. I saw a nice GSX650 (not gsxr) at a shop the other day, just thinking maybe same result with my GS without dropping $5-7K for a new bike.  I'm also 41 years old and dont want to bend over the bars any lower than my GS.

Do a couple of mods, drop  a tooth or two ride for a while and if your still unsatisfied go to a 650 or even a 750. But most of us agree its not worth the money or time to put a 650 into the 500. Anything can be done with money, time, and know how or sutible experimentation.

GR650 motor will fit the GS frame ... what else needs to be done to get it to run ... I dunno I am not there yet ... i just stuffed one in ...
Cool.
Buddha.