[UPDATE 2011-12-23: read the comments for good news.]

I few months ago I migrated my 10,000+ Flickr photographs to SmugMug, and deeply regret it.  So I’m sharing the problems just in case my pain can help others:

1. Filenames are lost.  The SmugMug migrator program is called Smugglr, and it transfers the “original” size in Flickr, which has a name like “4506134808_20b673be79_o.jpg” instead of whatever it was prior to uploading into Flickr (e.g., “Charles_Darwin_with_a_younger_woman_1860.jpg”).  This doesn’t seem like a big deal, but if you ever want to download the file from SmugMug onto your hard drive, the file is hard to find if your desktop has other files with “_o.jpg” at the end.  Similarly, if you have clients/friends who download your photographs, they don’t benefit from a useful filename.  Also, Google will probably never rank “4506134808_20b673be79_o.jpg” high in an image search even if the image is awesome, and even if you have great caption and keywords.  I’m not sure how Google computes rankings, but I suspect there are algorithms that compare filename data to keywords and search terms.  All of this is not Smugglr’s fault, though — I’m sure the programmer would have used the original filename if Flickr had made it available.  By the way, there is no way to change a filename within SmugMug, short of downloading the image, renaming it, and then replacing original (seems like it would take SmugMug all of a day to batch-enable that procedure…).
2. Images transferred from Flickr are probably lower quality than your originals.  Flickr restricts size and filetype, so if your camera was producing huge TIFF or RAW files all those years, Flickr constrained your uploads to 10mb/file and required them to be JPGs, GIFs, or PNGs (all fine for internet viewing, of course).  So Smugglr will send over to SmugMug a file that is not as good as the original file that is hopefully still lurking in your Aperture or Lightroom library.   If people find an image of yours on SmugMug and want to buy a $200 wall mural, you’ll be sad if they used a small JPG. Again, not a Smugglr problem, but a problem nonetheless, and one that I didn’t think about deeply enough at the time.
3. Images are duplicated in a messy way.  You might have an image that showed up in 3 different albums in Flickr, and because Smugglr will transfer each album in its entirety, you end up with 3 copies in 3 different SmugMug galleries.  If you change settings on 1 of those versions, those changes are not linked to the others.  So you really need to go and find the duplicates and potentially delete them.  Endlessly annoying.  There is no easy way to find these duplicates.
4. In the Smugglr transfer, all my keyword phrases were squished into single keywords with no spaces.  E.g., “United States” became “unitedstates.”  You can batch fix this in SmugMug, but it’s a pain and the “replace” action needs to done for each gallery, and for each phrase.  Terribly annoying.
5. Smugglr added a number and an alphanumeric as keywords to each photograph.  E.g., “82170932 b7c0b70ea8.” There’s a batch way to remove numbers, but, again, only one gallery at a time.  There’s is no way to automatically remove alphanumerics, so if you have 10,000 images, that’s 10,000 clicks (actually, more). I’ve been informed another SmugMug user that there is a way to prevent these numbers from being added, but I don’t think the settings would be apparent to any newbie thinking about migrating their photos (e.g., I still don’t understand how to do it!).
6. Photo descriptions in Flickr are not transferred.  So if you had elaborate thoughts about an image, you’d need to go back to the Flickr page and copy and paste over to SmugMug version.  If you have less than 100 photos, that might be an OK use of your day.  But if you have tens of thousands, that’s not a good use of your year.
7. The less obvious problem is that once you have all the albums converted to galleries on SmugMug, you’ll probably want to organize them in Categories and Sub-categories.  If you are used to the drag-n-drop simplicity of Flickr, you’ll quickly become sad with the equivalent actions on SmugMug, which seem trapped in code amber from the early 1990s. So if you have hundreds of galleries, creating categories and then finding the galleries to add to those categories is laborious and frustrating.  And if you ever want to alter those categories and their resident galleries in the future…you’ll be daydreaming about Flickr’s Organizer, which is almost fun to use.

So, after months of discovering the problems above, I think I’m going to delete my 10,000+ SmugMug photographs and slowly re-upload from the originals in my Aperture library. I could “replace” each photo individually, but that process doesn’t fix the keyword problem.

Anyway, hope the above might help somebody, and if you are wondering why my photo site is empty, that’s why. I’m still a fan of SmugMug, but not a fan of migrating photos there.