I've got a pair of Shimano BR-M355 that need new pads, front and rear. Went to the LBS, they actually said "we're having a hard time getting Shimano parts in stock, you should look online."

Shimano says the replacement pad is B03S. They also have an information page about counterfeit pads that also mentions that B03S is the equivalent replacement for B01S since 2017. However, I have an email receipt that says last time the LBS sold me new pads for one of these brakes it was M05.

Now I'm seeing B01S all over eBay pretty cheap, seemingly genuine, if the Shimano-looking packaging is to be trusted. (There's also super-cheap listings like this that don't quite claim to actually be B01S, and I don't trust). And there's M05, which looks identical to B01S/B03S (and fit fine from the last pad change)

Recommendations?

I'm leery of almost anything on E-bay. I'd contact one of the reputable on-line retailers like Jenson, Performance/Nashbar, Colorado Cyclist, Excel, etc. and get their recommendation and stock situation. Shimano may have several pad SKUs for a given brake model based on pad composition such as organic, metallic, etc.

Why the 'eek' face? Shops have been out of everything for over a year, it's nothing new. We've been telling customers the same thing the whole time. Especially with Shimano stuff, bike shops can only order it from Shimano or QBP.

With all the different compounds available I would think there would be many part numbers for pads that will fit. I prefer organic simply because I've had better luck with them not squealing.

What you see online may or may not be legit. There are multiple supply lines in the bike industry. It's been frustrating working at a shop when things are available to consumers (often parts intended for the OEM market moved into the gray market) but not available to consumers. I would personally rather use a well-known 3rd party brand (Kool Stop, for example) from a mainstream vendor than a possibly counterfeit pad from eBay or the like.

That pad shape is extremely common. They're on most entry level Shimano calipers and also most entry level Tektro, amongst a bunch of other smaller brands. I usually have stocked B01S/B03S because they're frankly normally inexpensive so why not go with the official Shimano parts, but given their unavailability I've been ordering a number of different 3rd party brands available through mainstream bicycle industry distributors like Koolstop and Tektro etc. They generally work fine.

M05 is, subtly, a slightly different shape.

If those M05s fit, that eBay seller looks pretty legit.

I'm just surprised a brick and mortar store would actually recommend buying online

Yeah, you know, that name does look familiar, and checking my email history, looks like I've ordered a lot of stuff from them before

Not unusual, we needed a derailleur hanger for a trek pretty fast and went to my Trek LBS, he told me the same thing, he had none in stock and unknown how long the back order was going to take to fill.

Only on-line dealer that had them and I trusted was in China, ordered last week, should clear customs early this week, should get it by the end of Jan +/-.....such is life