I'm using ISO's for the games.. here are my settings.
GSDX
[Settings]
Renderer=3
Interlace=0
AspectRatio=0
upscale_multiplier=1
windowed=0
filter=2
paltex=0
vsync=0
logz=1
fba=1
aa1=0
nativeres=0
resx=1024
resy=1024
swthreads=1
msaa=0
UserHacks_AlphaHack=0
UserHacks_HalfPixelOffset=0
UserHacks_SkipDraw=0
allowHacks=0
PCSX2
MainGuiPosition=450,255
SysSettingsTabName=Plugins
McdSettingsTabName=none
AppSettingsTabName=Plugins
GameDatabaseTabName=none
LanguageId=0
RecentIsoCount=12
DeskTheme=default
Listbook_ImageSize=32
Toolbar_ImageSize=24
Toolbar_ShowLabels=enabled
CurrentIso=C:\\Azureus Downloads\\[PSX PS2 ~ ITA] Final Fantasy VIII\\[PSX PS2 PSP ITA] Final Fantasy VIII\\FFVIII_DISC_1\\FFVIII_DISC_1.mdf
CurrentELF=
EnableSpeedHacks=disabled
EnableGameFixes=disabled
McdCompressNTFS=enabled
CdvdSource=Iso
[MemoryCards]
Slot1_Enable=enabled
Slot1_Filename=Mcd001.ps2
Slot2_Enable=enabled
Slot2_Filename=Mcd002.ps2
Multitap1_Slot2_Enable=disabled
Multitap1_Slot2_Filename=Mcd-Multitap1-Slot02.ps2
Multitap1_Slot3_Enable=disabled
Multitap1_Slot3_Filename=Mcd-Multitap1-Slot03.ps2
Multitap1_Slot4_Enable=disabled
Multitap1_Slot4_Filename=Mcd-Multitap1-Slot04.ps2
Multitap2_Slot2_Enable=disabled
Multitap2_Slot2_Filename=Mcd-Multitap2-Slot02.ps2
Multitap2_Slot3_Enable=disabled
Multitap2_Slot3_Filename=Mcd-Multitap2-Slot03.ps2
Multitap2_Slot4_Enable=disabled
Multitap2_Slot4_Filename=Mcd-Multitap2-Slot04.ps2
[ProgramLog]
Visible=enabled
AutoDock=enabled
DisplayPosition=835,255
DisplaySize=680,560
FontSize=8
Theme=Default
[Folders]
UseDefaultPlugins=enabled
UseDefaultSettings=enabled
UseDefaultBios=disabled
UseDefaultSnapshots=enabled
UseDefaultSavestates=enabled
UseDefaultMemoryCards=disabled
UseDefaultLogs=enabled
Plugins=plugins
Bios=D:\\Users\\Admin\\Documents\\PCSX2\\bios\\ps2bios
Snapshots=D:\\Users\\Admin\\Documents\\PCSX2\\snaps
Savestates=D:\\Users\\Admin\\Documents\\PCSX2\\sstates
MemoryCards=D:\\Users\\Admin\\Documents\\PCSX2\\memcards
Logs=D:\\Users\\Admin\\Documents\\PCSX2\\logs
RunIso=C:\\Azureus Downloads\\NBA 2K11 [MULTI5][PS2DVD][
WwW.GamesTorrents.CoM]
RunELF=D:\\Users\\Admin\\Documents\\PCSX2
[Filenames]
GS=D:\\Program Files (x86)\\PCSX2 0.9.7\\Plugins\\gsdx-sse2-r3878.dll
PAD=D:\\Program Files (x86)\\PCSX2 0.9.7\\Plugins\\lilypad-r3878.dll
SPU2=D:\\Program Files (x86)\\PCSX2 0.9.7\\Plugins\\spu2-x-r3878.dll
CDVD=D:\\Program Files (x86)\\PCSX2 0.9.7\\Plugins\\cdvdGigaherz.dll
USB=D:\\Program Files (x86)\\PCSX2 0.9.7\\Plugins\\USBnull.dll
FW=D:\\Program Files (x86)\\PCSX2 0.9.7\\Plugins\\FWnull.dll
DEV9=D:\\Program Files (x86)\\PCSX2 0.9.7\\Plugins\\DEV9null.dll
BIOS=D:\\Users\\Admin\\Documents\\PCSX2\\bios\\ps2bios\\scph39001.bin
[GSWindow]
CloseOnEsc=enabled
DefaultToFullscreen=disabled
AlwaysHideMouse=disabled
DisableResizeBorders=disabled
DisableScreenSaver=enabled
WindowSize=949,897
WindowPos=263,22
IsMaximized=disabled
IsFullscreen=disabled
AspectRatio=4:3
[Framerate]
NominalScalar=1.0
TurboScalar=2.0
SlomoScalar=0.50
SkipOnLimit=disabled
SkipOnTurbo=disabled
[EmuCore]
CdvdVerboseReads=disabled
CdvdDumpBlocks=disabled
EnablePatches=enabled
EnableCheats=disabled
ConsoleToStdio=disabled
HostFs=disabled
McdEnableEjection=enabled
MultitapPort0_Enabled=enabled
MultitapPort1_Enabled=enabled
[EmuCore/Speedhacks]
EECycleRate=0
VUCycleSteal=0
fastCDVD=disabled
IntcStat=enabled
WaitLoop=enabled
vuFlagHack=enabled
vuBlockHack=disabled
vuMinMax=disabled
[EmuCore/CPU]
FPU.DenormalsAreZero=enabled
FPU.FlushToZero=enabled
FPU.Roundmode=3
VU.DenormalsAreZero=enabled
VU.FlushToZero=enabled
VU.Roundmode=3
[EmuCore/CPU/Recompiler]
EnableEE=enabled
EnableIOP=enabled
EnableVU0=enabled
EnableVU1=enabled
UseMicroVU0=enabled
UseMicroVU1=enabled
vuOverflow=enabled
vuExtraOverflow=disabled
vuSignOverflow=disabled
vuUnderflow=disabled
fpuOverflow=enabled
fpuExtraOverflow=disabled
fpuFullMode=disabled
StackFrameChecks=disabled
PreBlockCheckEE=disabled
PreBlockCheckIOP=disabled
[EmuCore/GS]
SynchronousMTGS=disabled
DisableOutput=disabled
VsyncQueueSize=2
FrameLimitEnable=disabled
FrameSkipEnable=disabled
VsyncEnable=disabled
LimitScalar=1.0
FramerateNTSC=59.94
FrameratePAL=50.0
DefaultRegionMode=ntsc
FramesToDraw=2
FramesToSkip=2
[EmuCore/Gamefixes]
VuAddSubHack=disabled
VuClipFlagHack=disabled
FpuCompareHack=disabled
FpuMulHack=disabled
FpuNegDivHack=disabled
XgKickHack=disabled
IPUWaitHack=disabled
EETimingHack=disabled
SkipMPEGHack=disabled
OPHFlagHack=disabled
[EmuCore/Profiler]
Enabled=disabled
RecBlocks_EE=enabled
RecBlocks_IOP=enabled
RecBlocks_VU0=enabled
RecBlocks_VU1=enabled
[EmuCore/TraceLog]
Enabled=disabled
EE.bitset=0
IOP.bitset=0
[ConsoleLogSources]
Devel=enabled
.EEout=disabled
.IOPout=disabled
.EErecPerf=disabled
.ELF=disabled
.SysEvents=disabled
.pxThread=disabled
[TraceLogSources]
.SIF=disabled
EE.Bios=disabled
EE.Memory=disabled
EE.Disasm.R5900=disabled
EE.Disasm.COP0=disabled
EE.Disasm.FPU=disabled
EE.Disasm.VUmacro=disabled
EE.Disasm.Cache=disabled
EE.Registers.HwRegs=disabled
EE.Registers.UnknownRegs=disabled
EE.Registers.DmaRegs=disabled
EE.Registers.IPU=disabled
EE.GIFtags=disabled
EE.VIFcodes=disabled
EE.Events.DmaCtrl=disabled
EE.Events.Counters=disabled
EE.Events.MFIFO=disabled
EE.Events.VIF=disabled
EE.Events.GIF=disabled
IOP.Bios=disabled
IOP.Memorycards=disabled
IOP.Pad=disabled
IOP.Disasm.R3000A=disabled
IOP.Disasm.Memory=disabled
IOP.Registers.HwRegs=disabled
IOP.Registers.UnknownRegs=disabled
IOP.Registers.DmaRegs=disabled
IOP.Events.DmaCrl=disabled
IOP.Events.Counters=disabled
IOP.Events.CDVD=disabled
[TraceLogSources/IOP.Disasm.COP2]
GPU=disabled
[DialogPositions]
CoreSettings_Pos=882,281
AppSettings_Pos=879,323
[MemoryCardListPanel]
ColumnWidth_Slot=48
ColumnWidth_Status=96
ColumnWidth_Size=72
ColumnWidth_Formatted=96
ColumnWidth_Modified=120
ColumnWidth_Created=120
ColumnWidth_Filename=256
[RecentIso]
Filename00=D:\\Users\\Admin\\Downloads\\psx roms\\Prepared games\\Final Fantasy VIII (E) (Disc 1) [SLES-02080].bin
Filename01=D:\\Users\\Admin\\Downloads\\psx roms\\Prepared games\\Hot Shots Golf 2 [U] [SCUS-94476]\\Hot Shots Golf 2 [U] [SCUS-94476].img
Filename02=D:\\Users\\Admin\\Downloads\\psx roms\\Prepared games\\MADDEN2005.img
Filename03=D:\\Users\\Admin\\Downloads\\psx roms\\Prepared games\\Twisted Metal 4 [U] [SCUS-94560].img
Filename04=C:\\Azureus Downloads\\MADDEN 11\\Madden11NTSC.iso
Filename05=C:\\Azureus Downloads\\[PSX PS2 ~ ITA] Final Fantasy VIII\\[PSX PS2 PSP ITA] Final Fantasy VIII\\FFVIII_DISC_1\\FFVIII_DISC_1.mdf
Filename06=C:\\Azureus Downloads\\NBA 2K11 [MULTI5][PS2DVD][
WwW.GamesTorrents.CoM]\\NBA2K11.iso