This question is rather hard to answer. Each of the emulators has its pros and contras.
This is my experience and my opinion. If you have something relevant to add - feel free to do so, I would welcome it.
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UAE for DOS
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Faster then the others
More options than in WinUAE interface
Supports Picaso (Amiga can use SVGA modes, true colours)
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WinUAE
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User friendly
You can use both computers at one moment and share HDD
Supports long filenames
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Fellow
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Should be faster in some operations because of optimized x86 code
Might be less suitable for OS applications (Workbench)
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If something doesn't work it may be worth to try another emulator or to change some settings.
The problem can be very often cured by changing Kickstart (try 1.3 for older games) because
as you perhaps know some games didn't run on Amiga 600 or newer without a kickstart cheat.
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