The difference is in the way not affects the sentence due to the presence of the to.

Why (not to use) Magic Quotes.

(Why not) use Magic Quotes.

In the former, the not negates the to use, making the meaning an explanation of why using Magic Quotes is not something you want to do.

In the latter, the not negates the why, making the meaning a rhetorical question

The difference is in the way not affects the sentence due to the presence of the to.

Why (not to use) Magic Quotes.

(Why not) use Magic Quotes.

In the former, the not negates the to use, making the meaning an explanation of why using Magic Quotes is not something you want to do.

In the latter, the not negates the why, making the meaning a rhetorical question

The difference is in the way you join the words together.

Why (not to use) Magic Quotes.

(Why not) use Magic Quotes.

In the former, the not negates the to use, making the meaning an explanation of why using Magic Quotes is not something you want to do.

In the latter, the not negates the why, making the meaning a rhetorical question

The difference is in the way not affects the sentence due to the presence of the to.

Why (not to use) Magic Quotes.

(Why not) use Magic Quotes.

In the former, the not negates the to use, making the meaning an explanation of why using Magic Quotes is not something you want to do.

In the latter, the not negates the why, making the meaning a rhetorical question