One major factor in whether you should use Motif, Qt, or GTK will be your programming experience: if you are already familiar with one, that will make your ArcObjects experience easier. In addition, each has both benefits and disadvantages.
Pros
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Motif
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GTK
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Qt
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"traditional" Unix look-and-feel
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multi-platform availability
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multi-platform availability
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well supported and documented
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widely used for newer projects
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widely used for newer projects
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pre-installed on Solaris
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easier to program
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easier to program
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long-established industry standard
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standard part of most Linux distributions
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standard part of most Linux distributions
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free licenses available
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active development
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active development
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flexible L-GPL license
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Cons
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Motif
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GTK
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Qt
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not very easy to program
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non-centralized support
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less flexible and/or costly licensing
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little active development
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documentation is lacking
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Unix-only availability
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no mature gui-builder
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dated design
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no mature gui-builder
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