I found a few threads regarding individual ones e.g. -stan, -grad but I’m looking to make a comprehensive list. These can be for cities/towns or countries.
There’s the aforementioned -stan and -grad, also:
-polis
-ville
-ford
-furt
-forth
-shire
-berg
-burg
-borough
-brough
-field
-kirk
-bury
-stadt
How many more can you come up with?
-ia
-ton
-wich, -wick
-bridge
-by
-cester
-chester
-ham
-market
-mouth
-ton
-town
-wick
-ette
Ones I came up with without resort to searching the net:
-mont (e.g. “Glenmont, MD”);
-lea/-ley/-leigh (e.g. “Overlea, MD”)
Others
-mere/-more
-cot/-cott
The first that comes to mind is -pool (Blackpool, Liverpool). Wikipedia has a pretty long list of prefixes, roots, and suffixes in British placenames: List of generic forms in place names in the British Isles - Wikipedia
-boro
-borough
-bourne
I come from Colorado. Places like Boulder, Denver, and Fort Collins don’t really apply. 
hmmm…
-over and -dover?
-ogue
Common on Long Island – Cutchogue, Patchogue, Aquabogue, Quogue,
-sex
-hampton
And not really a suffix per se, but it serves a similar purpose: “Heights.”
-church
-land
Common?
Essex, Sussex, Middlesex, Wessex. Maybe I’ve forgotten one… but that’s still a pretty short list! 
-port
-ford
In India:
-pore/-pur (Jadavpur, Kidderpore, Barrackpore)
-nagar
-abad (Ahmedabad, Faridabad). These names only show up in areas that were once under the Mughals.
-thorpe - this is a viking suffix, quite a few of those around here.
beck - is another viking one
dale
gate
pool
-neck (Aquidneck, Mass.)
-by the Sea (Manchester-by the Sea, Mass.)
-sur-Mer (Villefranche-sur-Mer, France
-head (Marblehead, Mass.)
-bury
-yard (Martha’s Vineyard)
-grove
-kill (in southeastern New York. From Dutch, I think, meaning stream. PETA got all up in arms about the town of Fishkill once, a few years ago, but there are tons of them.)
-ia. Alexandria, Venezia, Albania, Monrovia, Bolivia, Brasilia…
The OP’s -stan is my favorite. Dave Barry once joked about a former Soviet republic named “Stanstanistan”.
Also sometimes spelled -otte. At least, in one case I can think of.
Which isn’t, technically, a place name, since it’s the name of a place that named after a woman.