Never alter the container you're looping on, because iterators on that container are not going to be informed of your alterations and, as you've noticed, that's quite likely to produce a very different loop and/or an incorrect one. In normal cases, looping on a copy of the container helps, but in your case it's clear that you don't want that, as the container will be empty after 50 legs of the loop and if you then try popping again you'll get an exception.

What's anything BUT clear is, what behavior are you trying to achieve, if any?! Maybe you can express your desires with a while...?

i = 0
while i < len(some_list):
    print i,                         
    print some_list.pop(0),                  
    print some_list.pop(0)

Since the loop below only modifies elements already seen, it would be considered acceptable:

a = ['a',' b', 'c ', ' d ']

for i, s in enumerate(a):
    a[i] = s.strip()

print(a) # -> ['a', 'b', 'c', 'd']

Which is different from:

a[:] = [s.strip() for s in a]

in that it doesn't require the creation of a temporary list and an assignment of it to replace the original, although it does require more indexing operations.

Caution: Although you can modify entries this way, you can't change the number of items in the list without risking the chance of encountering problems.

Here's an example of what I mean—deleting an entry messes-up the indexing from that point on:

b = ['a', ' b', 'c ', ' d ']

for i, s in enumerate(b):
    if s.strip() != b[i]:  # leading or trailing whitespace?
        del b[i]

print(b)  # -> ['a', 'c ']  # WRONG!

(The result is wrong because it didn't delete all the items it should have.)

Update

Since this is a fairly popular answer, here's how to effectively delete entries "in-place" (even though that's not exactly the question):

b = ['a',' b', 'c ', ' d ']

b[:] = [entry for entry in b if entry.strip() == entry]

print(b)  # -> ['a']  # CORRECT

See How to remove items from a list while iterating?.

You are not modifying the list, so to speak. You are simply modifying the elements in the list. I don't believe this is a problem.

To answer your second question, both ways are indeed allowed (as you know, since you ran the code), but it would depend on the situation. Are the contents mutable or immutable?

For example, if you want to add one to every element in a list of integers, this would not work:

>>> x = [1, 2, 3, 4, 5]
>>> for i in x:
...     i += 1
... 
>>> x
[1, 2, 3, 4, 5] 

Indeed, ints are immutable objects. Instead, you'd need to iterate over the indices and change the element at each index, like this:

>>> for i in range(len(x)):
...     x[i] += 1
...
>>> x
[2, 3, 4, 5, 6]

If your items are mutable, then the first method (of directly iterating over the elements rather than the indices) is more efficient without a doubt, because the extra step of indexing is an overhead that can be avoided since those elements are mutable.