Apologies for posting on a closed thread (Thank you Dark) but I want to share my opinion after reading the comments. I want to say right up front that I would have closed the thread but Dark Wolf was faster.
The main reason is... precision. You started by asking "which is the best", which means you don't know the answer (cause it would be pointless to ask a question that you know the answer to, right?). As people were providing their opinion, for right or wrong reasons you argued about them, which transformed the subject from, "which is the best" to "I have an issue with multiboot and few OS", which I call sidetracking and going off-topic, which yourself set. Even when people were answering the first part of your question "Which is the best app to burn ISOs on a USB stick" your own answers were changing the subject.
Clearly, before your post, you tried the software mentioned by others, and over time, the thread slowly shifted from your original question to the issue with files getting fragmented (the CONTIGUOUS you mentioned) which has nothing to do with the program you use or its popularity, but with the way, some OSes that write temp files to the USB should be treated and prepared for such use.
My advice is, next time go straight for the issue you have and don't sidetrack it yourself. That helps you to get better and higher quality answers, and most often solutions, and other members in the future who might have the same question as you will get better info.
Another 2 cents.