Appropriate way to store data in R
Without more information all I can say is that:


the say you're storing it is fine in general 
you can further transform/store your data depending on your use case


To expand on #2, if I want to study Distance vs Energy across all subjects, then I would format my data like this:

&gt; library(reshape2)
&gt; dt2 &lt;- dt[dt$measurement %in% c('Distance','Energy'),]
&gt; dt_cast &lt;- dcast(dt2, subject+Try~measurement+speed+condition, value.var='result')


The transformed data (dt_cast) would then look like:

  subject  Try Distance_speed1_Control Distance_speed1_Experm Distance_speed2_Control
1       1 Try1                       1                      3                       5
2       1 Try2                       2                      4                       6
  Distance_speed2_Experm Energy_speed1_Control Energy_speed1_Experm Energy_speed2_Control
1                      7                    21                   23                    25
2                      8                    22                   24                    26
  Energy_speed2_Experm
1                   27
2                   28


Allowing me to, for example, look at the relationship between the Distance_speed1_Control vs Energy_speed1_Control columns.

Basically subset/aggregate your data and then use the dcast to get the rows and columns the computer needs.