Well it depends what is the intended use. A quite good one is NutriSurvey that you can download for free from http://www.nutrisurvey.de/. Still, different software are linked to different food compositions databases and that is the key issue you mast have in mind.  So, if you plan to use it for nutritional adequacy assessment (especially for micronutrients) it is essential that you choose the one linked to food composition data that would best match the actual composition of food from your market. That means it would be ideal to use your national food composition data if it is available. If not, than you should at least try to use data from other country with similar food production technologies and food legislation (in respect to mandatory food fortification). On the other hand, if the intended use of the software is to track changes in personal macronutrient and energy intake, than I would say the best software is the one that is free and has at least one reliable reference. 

I hope this will help you

Best of luck!

http://www.fao.org/infoods/infoods/software-tools/en/

Thank you both. I actually tried NutriSurvey a while ago using an adjusted French food composition database, it is very easy to use, but it doesn't work on Linux. I'm using Ubuntu and can't find any alternatives.

The list by FAO is very useful though. Thanks.

Ali