It's probably very hard to decide, since there are so many wonderful episodes, but I tried to make a top 10 list of Lisa episodes. I really can't decide which one is number one, but I'll try to sort them at least a bit.

Separate Vocations

This one definitely has to be one of my all-time favorite episodes, and actually, it's the key episode that finally made me a Lisa fan when it was first aired in Germany about 1993. Somehow, I always liked Lisa when she's trying to break out from her usual self, and so seeing her a bit mischievous, almost playing the role of Bart, left a rather huge impression on me that wednesday in late january 1993.

The Summer of 4 Ft. 2

I always liked the "summer" themed episodes as well, and obviously, this is a direct continuation of Lisa breaking out of her usual habits, trying to imitate the "cool" behavior of her brother. Her new friends are wonderful, and this episode is filled with an endless amount of great gags as well.

Lisa's Substitute

Possibly one of the most emotional episodes ever made, and together with "Stark Raving Dad" this is probably the best usage of a guest star ever. Mr. Bergstrom is the teacher who every school kid would like to have, and the ending is just heartbreaking and heartwarming at the same time. Everytimes I see it, I can't really help to shed a tear or two (or even more ).

Lisa on Ice

Seeing Bart and Lisa teaming up and fighting together as siblings rather than against each other is always heartwarming, and this is probably the episode where it's shown at its best. One of the truly unforgettable moments of the entire show.

Lisa's Rival

The idea of introducing someone who is even smarter than Lisa was a great move, and I also like the fact that Allison still shows up now and then in the background, unlike other one-time characters, like Alex, Jessica or Greta (yes, I know that some may have shown up now and then, but not that frequent as Allison). It's also wonderful to see that Lisa and Allison finally became friends, after their initial rivalry.

Lisa's Sax

This episode is just wonderful, from the beginning to the very end. Young Lisa is simply adorable, and the Gerry Rafferty song at the end could play forever.

Lisa's Wedding

Like the "summer theme" episodes, those that are showing either the past or the future are somewhat special, and this is definitely the best "future" episode so far. The older Lisa looks terrific, and there are so many great ideas and jokes in this episode.

Moanin' Lisa

Maybe I should have mentioned this episode earlier above, but as I said, I can't really make an order within this top 10 list. It's truly one of the gems in the very first season, and although the characters weren't that well developed back then, the producers really nailed down Lisa's personality in this episode. Back in the Tracey Ullmann time, she wasn't much different than Bart, but I guess I can speak for everyone when I say that this change was the best thing they could have done for the whole show. 

Lisa Gets an A

For my coming of age ceremony (aka. confirmation), I chose a bible motto that could be paraphrased as "You will only get the victory if you played fair." This episode is a perfect example for this motto, and I'm sure everyone of us was confronted with a similar situation at least once. Again, this episode is showing a bit of Lisa's "dark side", and that's she's not perfect after all. But it makes her human, and that's what counts.

Little Girl in the Big Ten

I guess I don't surprise anyone by stating that the quality of the show has rapidly declined after the 9th or 10th season, but now and then, a gem can be found within the lake of mediocrity. This episode is one of them, and it surely has the same "feeling" like many of the old classics. Seeing Lisa in pure bliss while attending college is just wonderful, and it's also quite funny how she's trying to cover her true identity.

Ok, hopefully, a few others will post their top 10 episodes as well, and I'm eager to read why you consider them as the best of the best. I know that it's probably hard to find a few words about each of them, but I encourage you to try it at least. 

For me it is this chart-list:

1. Lisa's Substitute
2. Lisas Wedding
3. The Summer of 4 Ft. 2
4. Lisas First Word
5. Secret War Of Lisa Simpson
6. Lisa on Ice
7. Moanin' Lisa
8. Round Springfield
9. Scuse Me While I Miss The Sky
10. [every other Lisa-Episode] 

1. Summer of 4 ft. 2 (everyone loves that... )
2. Lisa's Substitute
3. 'Round Springfield (Lisa sang pretty well!)
4. Lisa the Simpson
5. Little Girl in the Big Ten
6. The President Wore Pearls
7. Future Drama
8. Lard of the Dance
9. She of Little Faith
10. Lisa the Vegetarian

For now, I'll do my top one.

1. Lisa's Wedding.

I'll do the other 9 later, I'm in an internet cafe and I'm not made of cash.

"Lisa's Substitute" is the best Lisa Episode and the best Episode ever, because I think this episode has the most enjoyable feeling, the most wonderful character (Bergstrom) and a wonderful ending with a very special father-like Homer. It is too complex to explain, lets just say, this episode is PERFECT!

"Lisas Wedding" has Lisa as a grown up women. And with a very good characterism. And also a extraordenary view to the future of the Simpsons. Love it!

"The Summer of 4 Ft. 2" shows a world, that really could never exist, but it is a charming story. Lisa, as a outsider, gets friends and the relationship between Bart and Lisa is told very interisting .

"Lisas First Word" is just explained in four words: "It is sooo cute!"

"Secret War Of Lisa Simpson" is especially uptodate, shows that Lisa would join a military society for the good. That confirmes my decision I made, to become a career soldier.

"Lisa on Ice" has the best story about the relationship of Bart and Lisa!

"Moanin' Lisa" is the first Lisa Episode, and the first bleeding gums episode and so moody! Love it!

"Round Springfield"... I think I don´t need to explain that! *crys*

"Scuse Me While I Miss The Sky" the best episode of the new generations. I think it deserves to be in the list. "Don´t you think you are overreacting, talking gumball machine?"

[every other Lisa-Episode]  is also great! 

I can't think of a top10, because all Lisa episodes are great, but the episode that's definitely my favorite is "Moaning Lisa". It has a nice and touching storyline, awesome music and a funny subplot. The scene where Lisa and Bleeding Gums Murphy are playing the sax on the bridge is easily my favorite moment of the entire series.

Other episodes like "Summer Of 4 Ft. 2", "Lisa's Sax", "Lisa On Ice" and "Lisa's Substitute" are also great episodes.

Yggdrasill
Hah, that was a great review! Thanks, it was a pleasure to read that.
I'm still not ready to do my list, just posting 10 episodes in a row is easy, I will try something more complex...

Paolo
A Star Is Torn episode is good by one's own way. The main thing I do like is Lisa's come out for healthy eating. And of course she's so cute when she sings her fisrt lullaby to all the family members. But the second part I don't like at all, sorry. All that singer's contest is something just a rubbish for me, with it's cynicism. I think the big showbusiness is not for her, she better that that. And can find her way to acknowledgement she wants so (not a cheap popularity like a pop-singer).