The company that I work for has and continues to put together some halfway decent web based applications, etc and I was wondering what are the prestigious / well-respected awards that I could submit our work to be nominated for.
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172answers:
2In all seriousness, don't. Save the time and efforts needed to submit and use it to improve your website generally.
Thank God that awards have largely disappeared from the web. Time was around 1998 when you couldn't move for Site A being 'best n site on the web' and Site B having 'Fred's Gold award for Webbiness'
Indeed there were notoriously places which you just went along to, submitted your site, and a day later they'd come back having 'claimed' to have reviewed your website and given it 5 stars for earth shattering goodness.
Result was piles of mediocre sites squeezing in lines of glitzy 'award' icons. Indeed displaying such a line of awards was almost always an indication that the site was pretty rubbish.
The only awards left which imho carry any weight at all are the Webbies. If you really need to submit something then these are the only ones worth your time - if you think you have a realistic chance of success then by all means do so, but I doubt 'halfway decent' will get you anywhere with these.