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I just purchased the Canon 40mm pancake lens for my 40D. I noticed that the barrel of the lens extends when focused close. Do I need to be worried about making sure the barrel is retracted before turning off and storing the camera?

Because this lens is focus by wire, turning the focus ring when the camera is off / asleep does not do anything. The only way to retract the lens is to focus on something at infinity or set it to manual focus and turn the ring before it turns off or goes to sleep. This seems like a lot of work and something I am going to frequently forget.

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All AF lenses are "focus-by-wire"... Also, Canon should return the lens to the home position when it's turned off. Surprising that don't do that. – BBking Nov 28 '12 at 0:52
I've been shoving it into my camera bag fully extended for weeks now, still works :P – dpollitt Nov 28 '12 at 2:39
1  
@BBking -- All? Even if that is true of all Canon EF/EF-S lenses, it's not exactly universal. There are an awful lot of Nikon, Pentax and Minolta/Sony lenses (as well as third-party lenses) in which the manual focus ring is directly connected to the helical focus mechanism (and sometimes there's a mechanical clutch). That is true of screw-drive lenses as well as some older micromotor designs. – Stan Rogers Nov 28 '12 at 3:18
OK. Although I'm not 100% sure exactly what models and lenses you're referring to, it sounds as if you're talking film? I don't recall any fully mechanical AF (Auto Focus) lenses ever been made. Please enlighten me with some! :) OK, all AF lenses in the past 10 years are "focus-by-wire". You kinda need the electronics to make it automatic. – BBking Nov 28 '12 at 11:03
2  
@BBking - again wrong. Nikon has just begun to replace their all-mechanical designs recently (the 50mm and 85mm f/1.4 & f/1.8 AF-S models are new in the last couple of years; the f/2.8 wide angles at 20, 24 and 28mm are still all-mechanical, as is the 35mm f/2). That's just in the Nikon line. Both Tamron and Tokina (along with the Tokina/Pentax DA* lenses) have current models that engage mechanical manual focus with a push-pull clutch, even if autofocus is signal-driven (rather than linkage-driven) from the body. AF doesn't imply no mechanical manual focus, even with USM-type lenses. – Stan Rogers Nov 29 '12 at 14:42
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Yes.

I imagine you'll be storing it in a bag or somewhere its not going to get bumped around, so there's no reason a lens needs to be in a special configuration for storage, other than to minimise space, but its not exactly taking up a lot of space either, even fully extended.

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