for perspecitive on my level of advice, could think of it perhaps as opposite of Edward_Stryfe's perspective.
I use to be really informed of these kind of issues, however my info maybe outdated or no longer apply to modern hardware.
The .ISO vs .BIN/.CUE, doesn't matter as far as I know... They are all CD/DVD image formats, it shouldn't matter which one you use, the formats use to only come into play when you Burn them to CD/DVD, but thats only because some of the Image formats are prorietary to the burning application, or server the application with copyrigth protection bypass info etc... None of which applies when your simply playing it off the Harddrive... Think of it similar to Video file containers such as .MP4 , .FLV , .HDMOV , .MKV , etc. It doesn't matter which your using as playback if they all encoded using the .h264 format, they will all Look the same.
and regaurding Edward's last paragraph, just fyi, nothing personal, your just ill informed... video playback for the most part has nothing to do with Emulation, or 3D graphic performance.
Its also a good time for me to point out I have no experience emulating PS2
tho I've heard INTEL cpu's are generally better for emulation, due to Emu optimizations on that platform, tho i have no clue if that specificly applies to PS2 Emus... Tho I also generally have known these past few generations, INTEL has been kicking AMD's ass in regaurds to perforamce efficency. Price per performance ratio may remain competitive tho.. you get what you pay for.
I also heard, the modern Integrated Graphics on the CPU Dies (I forgot the term) is actually better than the cheapo after market cards. Not like the old Onboard Graphics which shared the same Motherboard, but Didn't share the CPU's Bus speed and resources, etc.
In my experience with past hardware, Disabling the "application controle" function in your advanced graphics properties from the desktop control pannel.. and then manually Turning off VSYNC, and switching to 16bit display mode, would litterally nearly double gameplay speed/performance. If you don't know how to set the app to run in 16bit display mode, forcing your desktop to 16bit mode, and then forcing the application to run in WINDOWED mode instead of FULLSCREEN, will force it to 16.
This may no longer apply to modern hardware, and there maybe a lot more options... However If lowering the most powerful resouce intensive options, shows little to No performance difference.. Thats a pritty good hit its CPU related and not GPU.