We (a small team of software engineers and flow cytometrists) built a new tool for flow cytometry panel design and recently released online. It's called EasyPanel (link below).
It goes one step beyond what other online tools offer by actually suggesting specific optimized panels based on user's requests and requirements. It does so through an algorithm that Ranks all possible panels according to certain criteria such as systematically minimizing spectral overlap (spillover) between fluorochromes in the panel (among others). It could propose optimized panels of up to 19 fluorochromes.
Please give it a try and let me know what you think at email@example.com