Python algorithm for identification of low-level jets (meteorology)
Naming the variables


wspd_matrix would be much easier to read if it were called wind_speed_matrix 
jetspd would be much easier to read if it were called jet_speed
jethgt would be much easier to read if it were called jet_height


Remove the numeric values in the code

0.8 and 2.5 appear quite often in your code. It is hard for someone without a domain knowledge to know what they stand for. And if you have to change them for some reason, this is error-prone. Why not just naming them (max_multiplier = 0.8 per example) at the beginning of the function ?

Redundant condition

if x&lt;0.8*maxspd and x&lt;maxspd-2.5


appears twice in your code. It represents a clear mathematical function :

if x&lt;min(0.8*maxspd , maxspd-2.5)


which is much easier to read (and picture mentally)

Redundant code

Something needs to be done about this three prints :

print 'Maximum found at time',t,'and level',i,'with speed',x,'m/s'
print 'Minimum found at time',t,'and level',i,'with speed',x,'m/s' 
print 'Minimum found at time',t,'and level',i,'with speed',x,'m/s' 


Maybe a 

print_local_optimum_found(type_optimum, at_time, at_level, at_speed)


Check the input

if maxflg and not minflg:
    print 'probably something wrong with NaNs'


Why waiting until the end of the program to realize something wrong happened ? If you know NAs cause trouble, just check the presence of NAs before

The algorithm itself

It is hard to suggest improvements now with every piece of code in the same function. If you fix all this, such improvements will become much more readable!