Firstly I would like to say that I haven't 100% read all the posts here, so sorry if I'm repeating some mentioned facts already.
Secondly, Lit has indeed given outstanding contribution here, great!
About the original question - without doubt, they could. All inter-war armies were trained exactly for 2 plans - War with the USSR or with Germany. If I remember correctly, Latvia even had plan if both would attack.. And I'm sure Poland had seperate plans if one of them attacked, but had no plan if both would attack at once.
About if Baltic States had fighting chance. As Lit already showed here, they definitely had. My personal speculation is that if there would have been organised resistence before occupation, USSR would show higher respect for this region and organise puppet state like in Poland, Bulgaria, etc, and like it planned to do for Finland (as I see unrealistic actually beating Soviet army totally in region so "desirable" by them, like finnish troops, Baltic armies would be definitely eventually beaten).
What I think nobody has written here are the numbers that Baltic States could have mobilized, if there would have been the political will for it. For Latvia the decision to not mobilize was made of course without any democratic considerations (very different from Finland) in few persons meeting with ultimate question "do we have fighting chance" and the answer from both generals "no". Actually, army was trained exactly for that. However, it was allways assumed that fighting would be "until" western help, thats why getting western help was so important during all interwar period and thats why probably generals said "no". And thats why so many in 1945 thought that UK (or even USA), the friends from Liberation War, will soon come, and help to beat the Soviets, with their fleets and planes. Also, Poland's campaign changed totally everything. It was not supposed to be be so so quick. So all Baltic states, to whom Poland's army was one to learn something from, were shocked (like everybody else).
However, the numbers that could be gained with the 24-72h mobilization plans -
Latvia 130'000-140'000 (plus 50'000 with outside material help) - (8 divisions from peacetime 4)
Lithuania ~140'000 (plus 100'000 with help) - (not sure, peacetime 5)
Estonia 80'000 (plus 60'000 with help) - (not sure of wartime plans, peacetime 3, though it has very short bourder to defend, so it probably had the highest amount of troops per km)
So without any help they combined would have ~300'000 to add to their existing forces (existing - 60'000-65'000) in definitely less then a week.
For such small nations there could be no "second chance" if battles would go bad, too little space to retreat to, so they were prepared to mobilize everything, and fight to the maximum at once. And the maximum to mobilize is - ~10%-20% of population, depending on how prosperous the country is or/and how many rich allies it has.
By western accounts, Estonian army though not armed the best, could be even capable of offensive opperations, at least, better then Lat & Lit. Though none of them were really trained for that.
To compare - Finland had ~250'000 troops in winter war, similar number of tanks and planes as Baltics.
And, Soviet Union needed ~1 month to attack Finland after talks broke. So the fastest that Soviet Union could attack Baltics would be middle or end of October 1939 - not the best wether for, as Finland showed, actually not too battle-capable army (appearently great purges, like many countries thought, indeed weakened Red army greatly).
The combined defencive budgets of all 3 Baltic States were somewhat smaller then Yugoslavia's, definitely larger then Finlands - but coordinated military cooporation was almost nonexistant - however, it is without doubt that with actual military operations starting, such cooperation - at least on local scale, would be quick to appear.
So, again, answering the question. Soviet Union had no woking blizkrieg in 1939, as Winter War showed. So mobilization would have happened even during war. Thus, would ~360'000 be capable to resiste against 120'000-150'000 that were on the borders? Definitely yes. At least till more Soviet troops would be sent in, and then probably for a month or two. (Finland, in winter time, resisted for some 100 days)
Would they be capable of resisting individualy with weak cooperation? Probably. At least few weeks.
Might Red army be strong enough to occupy Baltics faster then in 72 hours and thus have to battle only the standing armies? I doubt it. If so, war might be over in a few days (and even that would be enough to have partial mobilization). However, Soviet army was supposed to enter Helsinki in 4 days.
So, my personal conclusion about Baltic States resisting would be - minimum 3-5 days (with Red army opperating "as intended" and not "as in Finland"), maximum - 2-3 months (too little supplies were collected to have prolonged war).
However, after signing treaty's for bases in 1939, winter was spent actively trying to buy heavy weaponery, understanding that tanks and planes have far outgrown their supposed roles. During war time it was particulary difficult with very little sellers, but still, at least Latvia managed to buy some heavy equipment. So if Baltics would have resisted in the summer of 1940,
1) no hope for international support, even moral one, since France was about to/had just fallen. (and Soviet Union used fall of Paris to occupy Baltics)
2) up to 20-30'000 thousands of russian troops on western side of the each country. (total at least 50'000)
3) many lessons learned by Soviet army from Finland.
However, even then there was a thought that maybe there should be resistance. But I think that in such a case, even though there were some plans to fight both the russians from west and east, war would be over in 2-3 days. A week would be very hard to believe.
So, I think it was 50 years of occupation that somehow printed in peoples minds that "there could have been no resistance". There could have, and in 1939 it would have worked.
P.S. very interesting, how Anchluss and events of march 1939 triggered events like, Mussolini wanting to show how powerfull he is, so he invaded Albania. And did Stalin wished to appear any weaker? Yea, right.
P.P.S. mobilized amounts of troops in Germany's and Soviet's armies from Baltic states represent approximetly how many could have been mobilized, more or less by their own governments.
P.P.P.S. I know that Latvians, though less and not as long as Lithuanians, also resisted up till ~mid 50ties, but I haven't heard if Estonians had armed resistance, I assume they probably did, maybe Lit knows?