I would second Phien's and La Boniche, both are very good, depending on what you are looking for.
Ricardo's Trattoria is upscale Italian with some New American touches. Very good specials, particularly seafood. Great bartending and live jazz on weekends. 110 Gorham St.
Pho Da Lat. Very solid vietnamese with a wide ranging menu. Soft shell crabs are excellent. Full bar with "chinese restaurant" drinks. 1575 Middlesex St.
Red Rose Restaurant. Cheap, authentic Cambodian. Haven't been in a few years, but have had nothing but good experiences. Fried whole fish is a specialty. 716 Middlesex St.
Udupi Bhavan and Mysore . Two vegetarian Indian places also on Middlesex St. Mysore is newer and has a bit more varied menu. Udupi has been around for awhile. The Chilli Baji at Udupi are great, fried hot peppers stuffed with chickpeas.
Udupi 1717 Middlesex, Mysore 1689 Middlesex.
Dorimar's Taqueria. Just a counter in a bar/nightclub downtown but great, unbelievably cheap taco's, burrito's and quesadillas. Large burritos are under 5 bucks and tacos are 1.50. 76 Merrimack St.
Cavaleiro's. Portuguese in a very nice atmosphere. Steak on a stone, pork with clams, and kale soup are all good.
573 Lawrence St.
I second Phien's Kitchen. Everything is fresh and Laotian food is very good.
I'm not a big fan of LaBoniche, although it has many fans because it's always busy on weekends. I find it too noisy and the food uninspired.
But I will suggest Red Rose for Cambodian. I think it's on Middlesex St. And Pho 88 for pho and for Shabu-shabu. It's on Westford St., just off Drum Hill.
Since you specifically aked for Southeast Asian or spicy, I'll leave it at that.
I don't know about "best", but two places I've been recently that were worthwhile:
Phien's Kitchen, a tiny, family-run Laotian place. We lunched on homemade sausages, a spicy papaya salad, a noodle soup with meatballs, and a chicken wing appetizer. Cheap, friendly, delicious. I drove there specifically because you can't find Laotian food (anywhere I know of) inside of I-495.
La Boniche, a long-running French place that I was happy to find was still good after revisiting for the first time in years. A lot of New American on the menu, and nothing to make you forget more authentic French places in Boston, but very nice for the neighborhood, with outsized portions, very good service, and modest prices.
You might want to repost on the New England board for more responses.
A recent post with the same question:
Heng Heng on Branch St. has replaced P&N, but basically the same stuff - banh mi and other take-out. Yummy, across the street, is also good for take-out and has some real good deals - large package of beef sticks with carrot/daikon salad and sticky rice for $5.00.
Here is an older post of mine that has other than Asian places I like - Osaka in Nashua has closed, but I think the others are still ok: