criscastells

I never trusted plate based real-time from the beginning. I would still go for the rotor based machines like Light Cycler 2 or RotorGene 6000

Cations stabilize the duplex state of DNA, and the algorithms for salt correction formulas are developed using Na⁺concentrations, for whatever reasons. So I'd take into account monovalent and bivalent ions as primer3 does it. I guess it's not that important if it's K⁺ or Na⁺ (someone might correct me here).
NH4⁺ surely also will have an effect as it is a cation, but it also influences the enzyme's activity. I don't know any program that accounts for that, but perhaps no data are available, as such additives are anyway a trial and error issue.
Actually my way to deal with it is to calculate roughly an annealing temperature (using standard settings) and then later doing a gradient PCR, if the reaction works. The calculated Tms are also always an estimate that have to be verified and then optimised. And also with simple formulas such as
T_m (°C) = 81.5 + 0.41(%GC) - (675/N) or T_m = 4(G + C) + 2(A + T) °C PCRs worked...