Museums with Axis equipment

There are several New Zealand museums with small Axis collections (one of which has that nifty little motorcycle halftrack) however I am assuming you are only looking for German items or Japanese as well.
Those Museums are quite hard to find actually. Many of the equipments were destroyed and melted down while the rest of the pieces are considered rare and valuable today.

Very interesting link though

Hope I can go to see
I dont know where you are geographically but I will what I know of

For tanks

The Tank Museum in Kabunka Russia.

The tank museum in Samaur France

The Patton Museum

Imperial War Museum has a few pieces but its not a complete
There is another Tank museum in Boyington UK but I dont know much about it.

For Aircraft

The RAF museum (this is the best) outside london
Le Bouget Meseum (outside Paris)
A very good museum in the Imperial War Museum at Duxford which served as a station of 12 group during the Battle of Britain.

There is an amazing collection of aircraft, armour, other vehicles, also a bouncing bomb of Dambusters fame.
Latrun Armour museum in Israel has a few WWIIgerman tanks in it. There are also a few still in the golan heights left over from 1967.